12 tags, 2862 commits
HEAD Mon Feb 8 12:02:54 2016 -0500 0 commits
2.2.0 Mon Feb 8 12:04:44 2016 -0500 405 commits
dbujold [email protected] 1 commits
dc03d86 Added link to the GenAP project in front page.
Edouard Henrion [email protected] 63 commits
477b332 Version bump to 2.2.0
caa197d Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
1d87ea7 BFXDEV-490 - updated base.ini files for chipseq dnaseq & rnaseq pipelines
371dd66 add report section in DNA-Seq High Coverage pipeline ini file
514d5b6 added guillimin specific ini file of DnaSeq_High_Coverage Pipeline - BFXDEV-490
be6d52a updated version of mugqic_tools.sh - BFXDEV-490 - BFXDEV-501
61ac85c ini file for PacBio Assembly pipeline is updated with new module versions - BFXDEV-490
042bb03 modules - updated vcftools VERSION in vcftools.sh - BFXDEV-490
f71fc01 minor update in module file created by perl.sh
d3c2bbf add report section in DNA-Seq High Coverage pipeline ini file
cd5d58c added guillimin specific ini file of DnaSeq_High_Coverage Pipeline - BFXDEV-490
7d0e6f0 updated version of mugqic_tools.sh - BFXDEV-490 - BFXDEV-501
7bf0a39 ini file for PacBio Assembly pipeline is updated with new module versions - BFXDEV-490
349ae58 modules - updated shebang for all the perl scripts installed by trinity.sh - BFXDEV-490
ab4b16d module - corrected SQLite archive url in trinotate.sh - BFXDEV-490
9e04f6a modules - updated vcftools VERSION in vcftools.sh - BFXDEV-490
e93f812 minor update in module file created by perl.sh
fe2a9cb rnaseq & rnaseqdn ini files updated after testings on guillimin - BFXDEV-490
39e91f1 add report section in DNA-Seq High Coverage pipeline ini file
e3bce29 added guillimin specific ini file of DnaSeq_High_Coverage Pipeline - BFXDEV-490
ecc918b Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
a4f7977 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
442830d updated ini files - BFXDEV-490
175b162 BFXDEV-490 - resolving conflict on guillimin
36b6f5d BFXDEV-490 - updated base.ini files for chipseq dnaseq & rnaseq pipelines
d1b51cb Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipelines
a3e2ab8 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
ec80af3 modules - updated vcftools VERSION in vcftools.sh - BFXDEV-490
b6e687a minor update in module file created by perl.sh
97bd155 Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipelines
682edbe mugqic_tools.sh VERSION=2.1.5, again...
fd3f0e3 updated version of mugqic_tools.sh - BFXDEV-490 - BFXDEV-501
424768a Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
4b4c08a ini file for PacBio Assembly pipeline is updated with new module versions - BFXDEV-490
f6415e1 modules - updated shebang for all the perl scripts installed by trinity.sh - BFXDEV-490
045c237 module - corrected SQLite archive url in trinotate.sh - BFXDEV-490
d2072f5 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
c22a596 modules - corrected typo in perl.sh when creating module file - BFXDEV-490
f89dbb3 modules/genomes - updated module version calls as well as database releases - BFXDEV-490
3970c21 Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipelines
17531c7 module - debugged scalpel.sh script - BFXDEV-490
a05c71b module - updated scalpel version - BFXDEV-490
1c9d868 module - debug in snap.sh - BFXDEV-490
eee7e56 module - updated version of Python (to 2.7.11) in gemini.sh - BFXDEV-490
8018094 module - removed module load calls in shortstack.sh - BFXDEV-490
8c69953 module - updated star.sh - BFXDEV
071a17b module - updated shortstack.sh snap.sh - BFXDEV
3fa5330 module - corrected typo in sphinx.sh - BFXDEV-490
976b856 module - vcftools updated version to 0.1.14 - BFXDEV-490
0d5709b module - debugged gemini.sh - BFXDEV-490
add9770 module - samtools updated to 1.3 - BFXDEV-490
15428f8 module - debug the name of the archive - BFXDEV-490
7ab3bbf module - UCSC version set to v326 instead of 'latest' - BFXDEV-490
16571fc update version of bwa module - BFXDEV-490
bf6422a some more updated modules - BFXDEV-490
0cf2a4d module & genome updates - BFXDEV-490
39c1758 module updates for to the release - BFXDEV-490
bb09f04 resources/modules/dev/epacts.sh has been removed (really)
0815aec resources/modules/dev/epacts.sh has been removed (really)
27058bc BFXDEV-490 - update of resources/modules/mugqic_tools.sh
0021aaa Merge branch 'gatk_variants' of bitbucket.org:mugqic/mugqic_pipelines into gatk_variants
a41229e gatk_variants - correct getDups() in ignstats.py so it ignores '?' as a dupplication rate when library ID is omitted - BFXDEV-481
b3ae471 gatk_variants - correct getDups() in ignstats.py so it ignores '?' as a dupplication rate when library ID is omitted
Edouard Henrion [email protected] 2 commits
839c464 updated chipseq.base.ini after mugqic_tools update - BFXDEV-501
476279f updated chipseq.base.ini after mugqic_tools update - BFXDEV-501
Francois Lefebvre [email protected] 2 commits
565ea8b BFXDEV-491, missing argument to re.sub for the SINGLE_END STAR commends case
bc9c0df Reverte back to older scheme. Was assuming bacteria only.
Francois Lefebvre [email protected] 37 commits
ae9667f Mammouth rnaseq ini required cluster_cpu=-l nodes=1:ppn=1 for new steps related to rRNA estimation
e21b18c -S flag was missing from the last samtools view command in the hard clip command
f5734af Install scripts
6eabc35 minor mod to R_Bioconductor (removed tabs in HERE DOCS)
432b3ab sleuth R package
93c3b1d Removed old R installation scripts
7758ea3 Added slash to URL to be able to retrieve latest Bioc version
b80611a sspace-longread dev install script
b626deb Kallisto install script (abacus only)
0f9449a popoolation install scripts modifications
dd9e031 more notes on pacts
1e9442f Added notes to EPACTS install script
ee112de Fastx and EPACTS install scripts
a1b5289 install scripts for ray, proved, sortmerna
a086744 Added celera and loRDEC install scripts
c56d297 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
01d05df Merge branch 'knitr_test'
62efc5f Added PBJelly install script + networkx python module
1691002 Fixed typos
394fca5 Replaced library calls in rmarkdown.py with direct ::render call. Added missing section header to exploratory report.
7d61414 no message
cf13caf Modified exploratory analysis report text
a8fd54f import rmarkdown in wrapper
abd9f89 damn dots
336b156 Testing out markdown::render paradigm
95df301 row.names=F for exploratory summary table
0f11b55 Working directory madness fixed
4de25fc Trying out rmarkdown::render() instead
22d5cc6 Trying html output
2c3caa8 knitr would set the wd to input document location...
c624897 dir.create problems
960c5e5 quotes missing
01e5ea5 no message
94b1e9b EOF is simpler
5742f00 Had forgotten the module calls
65e698e knit for exploratory + other changes
39f86fe Created Platanus install script
Gary Leveque [email protected] 2 commits
248c455 pacbio_assembly.base.ini edited online with Bitbucket
93cfad1 pacbio_assembly.base.ini edited online with Bitbucket --changed smrtanalysis_version = 2.3.0.140936.p2 to: smrtanalysis_version = 2.3.0.140936.p4
[email protected] [email protected] 1 commits
2d582b4 changes necessary for bacterial RNAseq using STAR --see BFXDEV-449
Johanna Sandoval [email protected] 52 commits
f7e38cb BFXDEV-405 correct single library issue in insilico read normalization
a745799 Merged in rnaseq_denovo_assembly_new_features (pull request #10)
b1ecdcc BFXDEV-397 resolved rebase conflict resources/modules/verifyBamID.sh
23a6e08 BFXDEV-397 PRJBFX-1187 added genome and software installs for verifyBamID, resolved issues from pull request #10
296aab1 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
91707a5 BFXDEV-397 resolved issues from pull requests # 10 https://bitbucket.org/mugqic/mugqic_pipelines/pull-requests/10/rnaseq_denovo_assembly_new_features removed dev modules
f80579a BFXDEV-397 resolved issues from pull requests # 10 https://bitbucket.org/mugqic/mugqic_pipelines/pull-requests/10/rnaseq_denovo_assembly_new_features
8ebbedb Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
d492790 BFXDEV-397 added spaces to table captions to goseq and dge filtered outputs
c03656d BFXDEV-397 added DGE and GOseq using filtereg contigs (based on trinotate annotations)
c22ce84 README.md edited online with Bitbucket
706303f BFXDEV-439 force installation or rmarkdown and knitr
ab8526c BFXDEV-439 resolved rebase conflicts rnaseq_denovo_assembly_new_features
716c646 BFXDEV-450 Change the mugqic_pipelines templates to add C3G logos and supporters
028430f BFXDEV-450 Change the mugqic_pipelines templates to add C3G logos and supporters
1905e38 BFXDEV-439 Reorganize rnaseq_de novo assembly to send all trinotate/rsem code to bfx libraries, commit new libraries
13cefa9 BFXDEV-439 Reorganize rnaseq_de novo assembly to send all trinotate/rsem code to bfx libraries, added trinotate annotations report, regenerated rnaseq_de_novo pipeline README markdown page
8d5737a BFXDEV-439 Reorganize rnaseq_de novo assembly to send all trinotate/rsem code to bfx libraries, added trinotate annotations report
b40353b BFXDEV-397 correct dependency problem in exploratory analysis using filtered isoforms
59fdc4e BFXDEV-396 added exploratory analysis using filtered transcripts. changed report markdown file
107fe2a BFXDEV-396 added exploratory analysis using filtered transcripts. changed report markdown file
b85f60b BFXDEV-396 added exploratory analysis using filtered transcripts
17e2143 BFXDEV-423 BFXDEV-399 BFXDEV-397 corrected blastx, abundance estimates to matrix and generated tabular and fasta filtered assembly using python SeqIO
de22cfa BFXDEV-432 define module picard rnaseq_denovo_assembly base ini
3820738 Merge branch 'rnaseq_denovo_assembly_new_features' of bitbucket.org:mugqic/mugqic_pipelines into rnaseq_denovo_assembly_new_features
f249f9c BFXDEV-397 rnaseq_denovo_assembly.py and rnaseq_denovo_assembly.base.ini rebased from master
9639c9f BFXDEV-397 corrected report exploratory analysis using knitr, tested using real data
1922f92 BFXDEV-397 tested filtered trinity output using real data (1 sample)
afad437 BFXDEV-397 component/contig filtering step based on annotations and predictions made by trinotate, added exploratory analysis based on raw counts generated by RSEM, modified differential expression analysis to use deseq and edger python libraries and to merge with annotations using mugqic tools parseMergeCsv
d223c74 detected bugs during tests
6d0e428 BFXDEV-396 add parse trinotate output to extract blast and go annotations for genes and transcripts
f91e427 BFXDEV-396 add GOseq analysis of annotated components in RNAseq de novo
c4597fa BFXDEV-396 add GOseq analysis of annotated components in RNAseq de novo
b2afc9e detected bugs during tests
bd91a58 BFXDEV-396 add parse trinotate output to extract blast and go annotations for genes and transcripts
2939c0e BFXDEV-396 add GOseq analysis of annotated components in RNAseq de novo
5ef76ae BFXDEV-396 add GOseq analysis of annotated components in RNAseq de novo
641a653 BFXDEV-397 corrected report exploratory analysis using knitr, tested using real data
cb1e022 BFXDEV-397 tested filtered trinity output using real data (1 sample)
d9a9c46 BFXDEV-397 merging conflicting versions of rnaseq_denovo_assembly.base.ini and rnaseq_denovo_assembly.py files
5c5b83e Merge branch 'rnaseq_denovo_assembly_new_features', remote branch 'origin' into rnaseq_denovo_assembly_new_features
62acde9 BFXDEV-397 fixing differences when rebasing from master
33d0dd0 BFXDEV-397 component/contig filtering step based on annotations and predictions made by trinotate, added exploratory analysis based on raw counts generated by RSEM, modified differential expression analysis to use deseq and edger python libraries and to merge with annotations using mugqic tools parseMergeCsv
d3e9ff6 detected bugs during tests
73ec341 BFXDEV-396 add parse trinotate output to extract blast and go annotations for genes and transcripts
8a0bb01 BFXDEV-396 add GOseq analysis of annotated components in RNAseq de novo
4d099e5 BFXDEV-396 add GOseq analysis of annotated components in RNAseq de novo
126102e detected bugs during tests
f9d902a BFXDEV-396 add parse trinotate output to extract blast and go annotations for genes and transcripts
0cb2d53 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines into rnaseq_denovo_assembly_new_features
5579bc4 BFXDEV-396 add GOseq analysis of annotated components in RNAseq de novo
ff1f6da BFXDEV-396 add GOseq analysis of annotated components in RNAseq de novo
lletourn [email protected] 18 commits
74503b2 Merge branch 'master' into highCoverageVariants
bfdf023 fixed io_buffer default
8b2cfcc BFXDEV-392 First implementation of high depth calling
d124958 BFXDEV-370 Fixed merging and output naming bugs
7381a03 Merge branch 'tumorPair' into highCoverageVariants
da6e1fb Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
fffb12b BFXDEV-392 need varscan for high coverage
4bdd553 Merge branch 'master' into tumorPair
8ae0dd3 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
23c3e59 set default ppn for igv to 2
bba9c56 BFXDEV-379 remove -gpfs from the ini files
6cf6ac4 Version bump to 2.2.0-beta
8e1345d BFXDEV-370 added merging step
27983c2 Merge branch 'master' into tumorPair
61e35f3 BFXDEV-370 Added indels and COSMIC
ffe5e6d BFXDEV-370 fixed scalpel script, added LD_LIB_PATH
8c0cfc7 BFXDEV-370 Added the scalpel module
7452be9 bvatools version bump
Mathieu Bourgey [email protected] 32 commits
a57fd6d RNASEQ - update ini downgrade R version for differential expression and java for rnaseqc - BFXDEV-490
129d564 RNASEQ - update ini downgrade R version for differential expression and java for rnaseqc - BFXDEV-490
4695881 RNASEQ - update ini downgrade R version for differential expression and java for rnaseqc - BFXDEV-490
226c59b RNASEQ - update ini downgrade R version for differential expression and java for rnaseqc - BFXDEV-490
1cbb0f1 chipseq - update module - BFXDEV-490
9e24486 dnaseq - add correct dependency in metrics snv - BFXDEV-508
501c3ac DNASEQ - remove bad ppn settings for mammouth ini file - BFXDEV-490
bc5920a RNASEQ - update ini downgrade R version for differential expression and java for rnaseqc - BFXDEV-490
849d732 RNASEQ - update ini downgrade R version for differential expression and java for rnaseqc - BFXDEV-490
db6c64a chipseq - update module - BFXDEV-490
65e3861 dnaseq - add correct dependency in metrics snv - BFXDEV-508
e1637bf DNASEQ - remove bad ppn settings for mammouth ini file - BFXDEV-490
c9e8db0 RNASEQ - update ini downgrade R version for differential expression and java for rnaseqc - BFXDEV-490
0d077aa RNASEQ - update ini downgrade R version for differential expression and java for rnaseqc - BFXDEV-490
32d1d5b Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
4c43bb2 chipseq - update module - BFXDEV-490
7a68160 dnaseq - add correct dependency in metrics snv - BFXDEV-508
7e2f61b Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
4a95aa1 DNASEQ - remove bad ppn settings for mammouth ini file - BFXDEV-490
58f9477 BFXDEV-465 - correct GATK DoC small bug to support when no bed fileis given in the readset file
269b60f DNAseq - Adding variant recalibration BFXDEV-436
557f75a DNAseq - gatk DoC will use the bed file as intervalls if the bed file is in the readset shett - BFXDEV-465
ce3014a DNAseq - implement haplotype caller and mpileup annotation and filtering using old foinction as background - BFXDEV-463
2aa0008 DNAseq - create new pipeline steps - BFXDEV-463
f46876a DNAseq - Add gvcf Combining the set of sample and genotyping - BFXDEV-440
157b7e9 DNAseq - starting to implement GATK gvcf merging - BFXDEV-440
3c407b2 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
74c6c2a Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
66cfdc6 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
bcfdd2c Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
c83d71c Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
1b17411 bump pacbio module to patch 4 - BFXDEV-415
mathieu bourgey [email protected] 105 commits
db54b51 resolving conflict
e7dc251 RNAseq - add specific older version of java for rnaseqc (support only 1.7)
3a2c22f resolving conflict
c554b5d resolving conflict
93a55f8 RNAseqDN - update module and remove trinity version check - BFXDEV-490
48fafb9 RNAseq - add specific older version of java for rnaseqc (support only 1.7)
2be21e1 Rnaseq_denovo_assembly - correct single library type bugs - BFXDEV-405
4103b9f DNASEQ - update SnpEff command for versuion 4.2 - BFXDEV-490
8e1bbc2 DNASEQ - support single end libray for metrics and dnasample metrics steps & allow filter_nstrech to use non recalibrated compress data - BFXDEV-503 BFXDEV-505
4e0cd6c resolving conflict
228c23a resolving conflict
6e42b3d resolving conflict
fea21f4 RNAseqDN - update module and remove trinity version check - BFXDEV-490
9cccf23 RNAseq - add specific older version of java for rnaseqc (support only 1.7)
50f9346 Rnaseq_denovo_assembly - correct single library type bugs - BFXDEV-405
71c233c DNASEQ - allow filter_nstrech to use non recalibrated compress data && update SnpEff command for versuion 4.2 - BFXDEV-505 ; BFXDEV-490
3a3c119 resolving merging conflict
a0491a4 RNAseqDN - update module and remove trinity version check - BFXDEV-490
ca27f3f RNAseq - add specific older version of java for rnaseqc (support only 1.7)
5b7e920 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
7481dc7 Rnaseq_denovo_assembly - correct single library type bugs - BFXDEV-405
b041650 DNASEQ - allow filter_nstrech to use non recalibrated compress data && update SnpEff command for versuion 4.2 - BFXDEV-505 ; BFXDEV-490
132e479 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
ffcee7d DNASEQ - support single end libray for metrics and dnasample metrics steps - BFXDEV-503
3f22b9d Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
10e4a0a updating modules (test on abacus human done) - BFXDEV-490
5de58e2 rnaseq - support fr-stranded single end library in wiggle tracks and metrics - BFXDEV-499
106788a Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
9b97e88 rnaseq - make wiggle tracks working for non UCSC genome ref - BFXDEV-498
9bb4b27 correct the version of pandoc - BFXDEV-490
e3f47cd update chipseq ini to latest version of modules - BFXDEV-490
ae112c0 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
f7b90b5 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
f0e0ee5 update human genome sh files - BFXDEV490
e3c6325 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
acc1d01 module - remove type in macs2 that make the module file invisible to the module system - BFXDEV-490
4c413a2 module - add gemini and bwakit modules - BFXDEV-490
c9a2f31 module - add star indexes for read length 75 and 150 bp - BFXDEV-490
14464b1 module - adding a step print for the module creation - BFXDEV-490
39f89bc module - add gemini and bwakit ; update bcftools htslib java picard prinseq-lite rnaseqc samtools - BFXDEV-490
b50d111 BFXDEV-490 - updating modules gnuplot ; hmmer; igvtools; macs2; pandoc; python_lib
61770a4 fixing conflict between master and highCoverageVariants branches
a3491eb BFXDEV-490 - updating modules bedtools; blast; gatk; ucsc
bd023c2 bfx/gatk.py - removing conflict to allow gatk_variants branch to be merged
292d51c Ressource - bump vcftools version to 0.1.14 - BFXDEV-489
13aa925 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
5b8a705 genomes - add rat Rnor_6 - BFXDEV-487
9ef56ce genomes - install genome by default in dev and in prod if argument MUGQIC_INSTALL_HOME is given - BFXDEV-485
4ac216d ressource - fix version of matplot lib to 1.4.3 for Qiime compatibility - BFXDEV-483
28175da gatk_variants - danseq - add mark_duplicates cleaning files - BFXDEV-471
1c06f0c gatk_variant - module - bump mugqic_tools install script to 2.1.3 - BFXDEV-484
62c067e Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
da7245b ressource - update python to 2.7.10 and add scikit-bio lib - BFXDEV-483
7c774e6 remove tumor_pair from highCoverage
5a20f1f DNAseq - add cleaning list to the new steps - BFXDEV-471
9266e03 DNAseq - change destionation path in the copy of SNV metrics zip file - BFXDEV-473
71b439e Pacbio assembly - modify whitelist option usage to do not generate additional ini and xml - BFXDEV-456
1f4eb9d Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
be62216 Bump module to the new smartanalysis patch 5
15b99f4 gatk_variants - add baits intervals file for picard_hs_metrics - BFXDEV-467
ad0a5c9 ingstats.py - Adding Array callrate check (Missing or Low) and add support for different manifest version through the -m option - BFXDEV-445 - BFXDEV-466 - BFXDEV-451
75379ef DNAseq - synchronize code and ini and correct runnning issue - BFXDEV-436 - BFXDEV-440 - BFXDEV-463 - BFXDEV-465
7a52905 DNAseq - remove some smalls dev typos and bugs - BFXDEV-436 - BFXDEV-440 - BFXDEV-463 - BFXDEV-465
a19894c PacBio - add require=False to the whitelist param - BFXDEV-456
e8223e6 PacBio - incorpore whitelist option during intial filtering - BFXDEV-456
53b2fbf PacBio - add addtionnal filtering config xml file for whitelisted assembly - BFXDEV-456
064ae2e PacBio - add specific ini file for whitelisted assembly - BFXDEV-456
8e298ef Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
7769b77 update bwa install script to the newer version
7261373 change star index place in resources/genomes/install_genome.sh
0904455 update install_genome.sh to use the coirrect version of R_packages
a3e0340 bump bos_taurus install script to ensembl 80
c57be72 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
94223ff bump bos_taurus install script to ensembl 81
17bea25 make ignstats poiting on nanuq (not QC nanuq)
382c952 Merge remote-tracking branch 'origin/processingReport'
051e378 RNAseq - repair missing dependency - BFXDEV-427
26d5d41 debug paired_tumor scalpel vcf merging
d2c011b removed merge conflicts
29a319b DNAseq - regenarate updated README.md
85017c1 DNAseq - change fixemate description text: picard -> bvatools
ba184cc High_coverage - needs dict2BEDs.py which is only in dev version of mugqic_tools - modifiy the ini file
3d88798 DNAseq - change post fixmate sorting to generate and indexed bam - BFXDEV-421
83e7e16 modify igvtools lib to allow modifiy paramter through the ini file - BFXDEV-419
d5d86bf Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
71c3d26 DNAseq - change coverage metrics report to remove the CCDS part of the table - BFXDEV-381
0de4e65 rnaseq add bam_hard_clip step : Generate a hardclipped version of the bam for the toxedo suite which doesn't support this official sam feature - BFXDEV-377 + change rRNA metrics output to avoid name conflict - BFXDEV-401 - BFXDEV-407
8a63681 update python and python lib to include Qiime ligth version installation - BFXDEV-412
8bb30ee bump trinity install script to version 2.0.6
1b2a34d rnaseq - remove tophat/botwie commented section and modules
f53ed32 rnaseq_denovo_assembly - correct single library issue and add in comment the correponding change in the base.ini - BFXDEV-405
d37b2c8 nanuq2mugqic_pipelines.py - support nanuq group info for Miseq/Hiseq/Pacbio technology - BFXDEV-418
b03537a update install module general script
2d1dbe4 bump smrtanalysis module to 2.3.0 patch 4
27bad46 update install module general script
006f59c update install module general script
08acf20 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
bcb9589 bump smrtanalysis module to 2.3.0 patch 4
ba4b9f1 update bvatools module for release 1.6
c72acd4 core/pipeline.py remove duplicates sections in reports - BFXDEV-388
4cb0ba7 ChipSeq - remove expected input files for broad peaks when generating homer annotation report - BFXDEV-393
797c968 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
3a54c85 modify resources/modules/smrtanalysis.sh for patch 3
ce104cd Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
d309b7d RESSOURCES - R_bioconductor - Addthe package 'circlize' to the list of R package to automatically install
mathieu bourgey [email protected] 6 commits
5db43a8 Merged in irp_end_fastq_notification (pull request #14)
de7d7f8 Merged in irp_bcl2fastq2 (pull request #13)
d3acddd Merged in illumina_run_processing_sprint (pull request #11)
82747c8 Merged in pacBio_whitelist (pull request #7)
e16e90d Merged in ignstats (pull request #8)
8e2cf4c rnaseq.base.ini increase star io limit to 4G by default
mmichaud [email protected] 62 commits
4d820a7 BFXDEV-504 - Notify nanuq when fastqs are completed for a lane (fix url) - illuminaRunProcessing
7ab569e BFXDEV-504 Notify nanuq when fastqs are completed for a lane
cdafb23 Fix alignment for lanes with a mix of samples with genomic database and no genomic database.
fd8579e BFXDEV-504 Notify nanuq when fastqs are completed for a lane (fix url)
7282b30 BFXDEV-504 Notify nanuq when fastqs are completed for a lane
2d9a896 Fix alignment for lanes with a mix of samples with genomic database and no genomic database.
e0be331 Fix alignment for lanes with a mix of samples with genomic database and no genomic database.
6e04c62 BFXDEV-504 Notify nanuq when fastqs are completed for a lane (fix url)
34ca19a BFXDEV-504 Notify nanuq when fastqs are completed for a lane
09ff700 Increase resources for qc.
3dfce03 BFXDEV-488 Illumina Run Processing: Use bcl2fastq2. Fix for dual-indexing.
5e8133e Use 2 core for rsync.
48a4bd8 Merge branch 'master' into irp_bcl2fastq2
a9560d4 Fine tune cluster settings according to the history of the jobs of the last three months.
b917ee5 BFXDEV-413 Fix code according to code-review.
a8fd8bf BFXDEV-488 Illumina Run Processing: Use bcl2fastq2.
be6ec3f Merge branch 'master' into illumina_run_processing_sprint
e0c3e20 BFXDEV-468 VerifyBamId: Fix job name when not using bed file.
ec19be9 BFXDEV-468 VerifyBamId: Run even we don't have a bed file.
1ffafbb BFXDEV-468 VerifyBamId: Use a version supporting "chr" in chromosome name.
dec09d8 BFXDEV-468 VerifyBamId: Fix output for nanuq.
eed1cc1 BFXDEV-468 VerifyBamId: Shorter job name.
750495f BFXDEV-468 VerifyBamId: Properly concat jobs
ce01a76 BFXDEV-468 VerifyBamId: Nanuq friendly output.
9d5fa0e BFXDEV-468 VerifyBamId: Don't use a compressed VCF + Nanuq friendly output.
c4bd81b BFXDEV-468 VerifyBamId: Add missing configuration.
72c77d2 BFXDEV-468 VerifyBamId: Fix annotation file name.
0001099 BFXDEV-468 VerifyBamId: Fix wrong genome for sample.
15a3a2b BFXDEV-468 VerifyBamId: Changes to the annotation filename.
7fc91bd BFXDEV-468 Don't run verifyBamId when there is no "dbnfp_af_field" on the genome.
d747ef6 Illumina Run Processing: Fix barcode counter path with cvmfs
68c0089 BFXDEV-468 IRP - VerifyBamId: Optional dbsnp_version and dbnsfp_af_field in genome ini file.
5a3fd82 Use cvmfs blast and bwa.
75af739 BFXDEV-468 Add verifyBamID in Illumina Run Processing
94ccde0 Merge branch 'master' into illumina_run_processing_sprint
7d6cf51 BFXDEV-447 Add rRNA estimate using silva blast database. (Fix change output file name)
dd9f3f7 BFXDEV-464 Don't use an hardcoded genome list for the alignment: parse the value from the sample sheet and validate that we have the genome on disk.
015435e BFXDEV-462 Output STAR bam in a unique folder to support lanes with multiple samples with the same name (fix redo of pipeline always restarting the STAR align).
f0ecd63 BFXDEV-447 Add rRNA estimate using silva blast database. (Fix error when creating result file)
2d39be9 BFXDEV-413 Add Estimated Genome Size from the nanuq CSV.
c73b3fc BFXDEV-447 Add rRNA estimate using silva blast database.
fdcb45e BFXDEV-462 Output STAR bam in a unique folder to support lanes with multiple samples with the same name.
1819bf2 Add sample sheets examples and add description about "Genomic Database"
be10d09 BFXDEV-457 BFXDEV-459 Update documentation.
b337a06 Don't warn when skipping alignment on a sample without "Genomic Database"
a73ca70 BFXDEV-459 Merge start_copy and copy steps.
583237b BFXDEV-457 Add the possibility to regroup all the md5 jobs into one (add "one_job=1" in "[md5]" config section).
56cdf2d BFXDEV-458 Fix mask calculation problem on lanes with nextera/truseq samples.
041d4e8 More useful usage message.
3cd065c Merge branch 'master' into irp_genomic_database
d90c137 Merge branch 'master' into irp_genomic_database
2f0ef65 Illumina Run Processing: Increase memory for BVATool DoC and Readsqc
a864f31 BFXDEV-369 Illumina Run Processing: Fix GRCm38 genome detection.
7eae59d BFXDEV-369 Illumina Run Processing: Use the reference specified in the request form
64fb218 Increase processors per node for Fastq and bwa alignment. Ignore setfacl exit code for the copy step.
fe44577 BFXDEV-417 IGNStats: Output identity value as ratio, not percentage (0.95 not 95.0) - Fix passFail threshold according to the new value.
cafa62c BFXDEV-417 IGNStats: Output Array Call Rate as ratio, not percentage (0.95 not 95.0%)
eb810e0 BFXDEV-417 IGNStats: Output identity value as ratio, not percentage (0.95 not 95.0)
3724583 BFXDEV-417 Modifiy IGN stats parser to allow the upload of data to a nanuq server.
ce52854 Use 13 core for BWA job to avoid excessive memory usage.
8505fab BFXDEV-385 Fix bed files handling in Illumina Run Processing.
29d5c0f BFXDEV-380 Change permissions of the run files on the destination.
[email protected] [email protected] 15 commits
ad55029 genomes - updated bash script for human genome GRCh37 and GRCh38 - BFXDEV-490
4d653bf Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipelines
d2fd863 Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipelines
e4b6339 Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipelines
1c79f7e Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipelines
36b260f Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipelines
5655027 Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipelines
7e8870a Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipelines
0a73d79 Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipelines
eb30107 Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipelines
8c32446 Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipelines
0b9b70c Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipelines
0233d70 mugqic_tools is now up to date && resources/modules/dev/epacts.sh has been removed
64c821d Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipeline
a65de9e temporary modify install_genome.sh to run the job in batch (job submission is blocked
ptranvan [email protected] 1 commits
2a1917b Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipelines
[email protected] [email protected] 4 commits
f184966 Addition of htslib module and resolved pull request comments
457c369 addition of vcf preprocessing, snpeff, gemini and ini adjustments
09ad7f1 addition of vcf preprocessing, snpeff, gemini and ini adjustments
05f05b2 Merge branch 'highCoverageVariants' of https://bitbucket.org/mugqic/mugqic_pipelines
Robert Eveleigh [email protected] 2 commits
60fd230 Merge branch 'highCoverageVariants' of bitbucket.org:mugqic/mugqic_pipelines into highCoverageVariants
76802ee Updates to pairedTumor: addition of CombineVariants
2.1.1 Mon Apr 13 22:23:46 2015 -0400 172 commits
Francois Lefebvre [email protected] 4 commits
65710dc QUAST and Minia dev install scripts
5b404f3 Updated kmergenie version in install script and moved to dev
6db368e Added NxTrim mugqic_dev install script
45b9fb0 Updated a bunch of module dev install scripts
Joël Fillon [email protected] 109 commits
4db053f Added Gorilla_gorilla.gorGor3.sh in resources/genomes/old/
deb0b82 Changed report job names with '_' instead of '.' to avoid scheduler cpu setting > 1
4d8b38a Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
b471f6f Fixed bug in RNA-Seq De Novo Assembly : use RSEM plugin in Trinity instead of external one
6c79dd4 README.md edited online with Bitbucket
2e53a76 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
455a50c Fixed missing pandoc module in rnaseq
0ffb7ea Added variables total and average read length in pacbio assembly stats report + changed locale from fr_FR to en_CA
70150e7 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
121faa0 Added sample_cutoff_mer_size to pacbio report job names
fcb6b89 README.md edited online with Bitbucket
272830b README.md edited online with Bitbucket
89c55cb README.md edited online with Bitbucket
8f6eeb7 Fixed cpu bug for blastp_transdecoder_uniprot job in RNA-Seq De Novo assembly
cae10e5 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
28eb954 Minor comment updates
2c4a463 README.md edited online with Bitbucket
c4262fa README.md edited online with Bitbucket
3f664a5 README.md edited online with Bitbucket
dc8ec12 README.md edited online with Bitbucket
c60d742 README.md edited online with Bitbucket
b38e195 README.md edited online with Bitbucket
6d4206c README.md edited online with Bitbucket
4a6982c README.md edited online with Bitbucket
39ee0b9 README.md edited online with Bitbucket
1f13501 README.md edited online with Bitbucket
0376786 README.md edited online with Bitbucket
43d0ac6 README.md edited online with Bitbucket
be50cd0 README.md edited online with Bitbucket
f85506e README.md edited online with Bitbucket
5e335b4 Added GNU Lesser General Public License (LGPL) to MUGQIC Pipelines
0b79b46 BFXDEV-59 Updated ChIP-Seq report redesign with sample metrics without trimming
ec88ea5 Fixed bug cluster_cpu for blastx_trinity_uniprot
5962a9f Removed UniRef BLAST in RNA-Seq De Novo Assembly since it is too long; factorized differential expression code; renamed design variable into contrast
611223e Adjusted Trinity butterfly cluster resources for RNA-Seq De Novo Assembly on abacus
371d60c BFXDEV-59 Completed ChIP-Seq report redesign
7eedd05 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines into report
01a41aa BFXDEV-59 ChIP-Seq report redesign
f8bf89f BFXDEV-59 Completed PacBio Assembly report redesign
479ea0b BFXDEV-59 Differential expression RNA-Seq De Novo Assembly report redesign commit
76c9bc3 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines into report
c7a9036 BFXDEV-59 More RNA-Seq De Novo Assembly report redesign commit
ac2daf3 README.md edited online with Bitbucket
e7f156a README.md edited online with Bitbucket
3caf504 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines into report
6771f03 BFXDEV-59 First RNA-Seq De Novo Assembly report redesign commit
5c858ad Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
5d82ab0 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines into report
94e9930 Decreased rnaseq cufflinks default pmem to 2700 for guillimin
79ea01b Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
80cfde8 Increased rnaseq cufflinks default pmem to 3700 for guillimin
9e655b9 Fixed BED file abspath in bvatools
c183fad BFXDEV-59 Completed RNA-Seq report redesign
61676eb BFXDEV-59 Added metrics steps for RNA-Seq report
e760ac7 BFXDEV-59 Fixed merge conflict
fbedae5 BFXDEV-59 More and more commit for partial HTML report
7a95c84 Increased dnaseq compute_effects ram
c6c7ead BFXDEV-59 Even more commit for RNA-Seq report
75b2a7e BFXDEV-59 Even more commit for RNA-Seq report
5da9885 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines into report
0463d00 BFXDEV-348 Fixed with readset name = <sample>.<library_barcode>.<run>.<lane>
3072da1 BFXDEV-59 Even more commit for RNA-Seq report
57f2aef BFXDEV-59 More commit for RNA-Seq report
ad7e670 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
be92407 Updated mugqic_tools to version 2.1.0
672b681 BFXDEV-59 First commit for RNA-Seq report
f194ec3 BFXDEV-59 DNA-Seq report minor fix
7f98cbf Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines into report
40a04d0 BFXDEV-59 DNA-Seq report redesign done + fix
b4b408f BFXDEV-59 DNA-Seq report redesign done
426e878 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines into report
a0b4223 Minor doc fix
bc1d662 BFXDEV-59 Even more report redesign commit
09de8ac BFXDEV-59 More report redesign commit
91e8e95 BFXDEV-59 First report redesign commit
77f66c4 Added UCSC genomes in install_all_genomes.sh
aa6a8e0 Create genome rrna.fa with grep -i 'rrna'... + remove variation sequences containing '.' in Ensembl vcf.gz which make GATK crash
525faa8 BFXDEV-295 Updated mugqic_R_packages to 1.0.3 for RNA-Seq De Novo pipeline
da8253e BFXDEV-295 minor fix for RNA-Seq De Novo pipeline
e161ad9 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
4d177be Updated Python pysam to version 0.8.2
e7ca27f README.md edited online with Bitbucket
48073ca README.md edited online with Bitbucket
70a0304 README.md edited online with Bitbucket
1e24257 Increased cores for homer_annotate_peaks in chipseq
3c2c24d Fix new section names for blast on uniprot in RNA-Seq De Novo pipeline
e699c64 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
aeedee4 Added chipseq in PATH of module mugqic_pipelines
7ce201c Added ccds filepath in Rattus_norvegicus.Rnor_5.0.ini
7b08143 BFXDEV-295 Moved trinotate Pfam + UniProt DBs in /nfs3_ib/bourque-mp2.nfs/tank/nfs/bourque/nobackup/share/mugqic_prod/genomes/[blast|pfam]_db/ for RNA-Seq De Novo pipeline
c47a519 BFXDEV-295 Update RNA-Seq De Novo pipeline with modules in prod and trinotate updated
33812be Minor mammouth adjustment regarding increased ram and core in snp_effect job for DNA-Seq Pipeline
9689e6d Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
c345049 Increased ram and core in snp_effect job for DNA-Seq Pipeline
8743bbb Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
9f5b422 BFXDEV-295 Updated RNA-Seq De Novo assembly pipeline with Trinity 2.0 and Trinotate 2.0
b484ff7 README.md edited online with Bitbucket
4b19c20 README.md edited online with Bitbucket
1b0f09c Minor fix in python lib install
9180612 Separated python install and python lib install + minor weblogo install update
e06560d Minor fix in Perl lib install
b202849 Fixed missing bvatools.depth_of_coverage other_options + snpsift_annotate module_snpeff=mugqic/snpEff/4.0 + minor uppercased '.insert_size_Histogram.pdf' for picard.collect_multiple_metrics output file in dnaseq pipeline
f8b35eb Fixed missing 'nodes=1' in pacbio_assembly.guillimin.ini smrtanalysis_run_ca
e7d4a0e Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
62a0e00 Updated bedtools to version 2.22.1
9328bc9 Standardized perl module install and moved CPAN libs in a different script
0fb4c64 BFXDEV-335 Removed adapter FASTA files except adapters-fluidigm.fa
4aba5c1 BFXDEV-335 Create adapter FASTA from readset file for Trimmomatic, if not defined in config file
ba78748 Version bump to 2.1.1-beta
lletourn [email protected] 14 commits
1792f2c Version bump to 2.1.1
8810822 BFXDEV-375 Fixed ram sorting issues when using star
e9fcf54 Merge branch 'master' into rna_metrics
a7e3465 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
8ba6662 BFXDEV-368 IGN script to extract stats
8f69140 Fixed code for tools that need to be downloaded manually like gatk
f6ee04e Updated gatk
4622df3 Updated samtools, bcftools, htslib
6eac315 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
a44561f BFXDEV-351 removed md5 from markdup and added it to recal
8abc6cc Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
1db78f9 BFXDEV-355 Removed CCDS from the options BFXDEV-356 added compression to haplotype caller output
9a0a698 BFXDEV-351 Removed MD5 from markdup, added it to recalibration
b33195c BFXDEV-346 Split jobs in a more uniform way
Mathieu Bourgey [email protected] 8 commits
70099f3 rnaseq - include correlation matrix manual estimation using an utils.py new function
fd53801 RNAmetrics - include ini_section argument to some bfs picard function to allow to use them several time with different parameter in the same ini
e7c5a01 rnaMetrics - remove confilct pipelines/rnaseq/rnaseq.base.ini
9ad7fbb rnaMetrics - update pipelines/rnaseq/rnaseq.py pipelines/rnaseq/rnaseq.base.ini
9d3b87d RNAseq - metrics update ini
1913bc1 RNAseq - remove conflict
deca058 RNAseq - metrics RNA - update base ini
2fc2006 RNAseq - remove rnaseqc; add picard_rna_metrics ; partial add estimate_ribosomal_rna - BFXDEV-345
mathieu bourgey [email protected] 9 commits
05937d6 RNA-seq - rna_metrics : test are ok; new files annoation files are created ; point to the production assembly folder - BFXDEV-345
b2c948b ressource -Genome install script add the creation of the ref_flat file format of the annotation from the gtf and correct a path in the GRCh38 file (All.vcf.gz) - BFXDEV-374
7d8f72f RNAseq- update module version not found in CVMFS (bowtie, bvatools, mugqic_tools) - BFXDEV-373
e57ed5e RNAseq- remove redundant step in the step initialization - BFXDEV-371
3138867 release new version of resources/modules/mugqic_tools.sh
9aa58f7 RNAseq - rna_metrics - finish the rRNA and rna metrcis modifications - BFXDEV-345
cd5f239 RNAseq -rna_metrics -fit the new bam2fq from bvatools_dev
d2048eb Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines into rna_metrics
d651fee RNAseq - rRNA metrics add bvatools | bwa | picard && rrnaBMAcount.py
mmichaud [email protected] 27 commits
2a821a4 bcl2fastq module name change.
00b481f Merge branch 'master' into irp_rna_metrics
c2c33a3 MPS-1740 Use updated production genomes.
5f3c74e MPS-1740 Use released version 1.5 of bvaTools
d191969 Increase STAR sort memory
dd936d0 BFXDEV-363 IRP: Don't copy phasing and matrix files.
ae9713b BFXDEV-353 IRP: Standardize job name
e83e25f Merge branch 'master' into irp_rna_metrics
87aaf0d Merging rna_metrics on irp-rna_metrics
b0dff3b BFXDEV-353 Use dev version of mugqic tools
f94c135 Merge branch 'master' into irp_rna_metrics
75398a3 BFXDEV-353 Use new version of rRNABAMcounter.
5f443d4 BFXDEV-353 Use a nanuq friendly name for the rRNA metrics file
ea661af BFXDEV-353 Add the rnaseqc '-rRNA' option to set an optional ribosomal rna interval list. Setting an empty file will skip the rRNA count.
91c0d87 Simplify illumina run processing RG tag logic. As library, run and lane are mandatory there is no need to validate that they exists.
4abaa7b BFXDEV-353 Fix bwa other_options
81e7423 BFXDEV-353 Use DEV versions of bvatools and genome. Update mugqic_tools to 2.1.0.
79a02a7 BFXDEV-353 Update rna-seq metrics according to rna-seq pipeline
081c6b8 Merge branch 'master' into irp_rna_metrics
fcc8392 Code format
d62f855 Merge branch 'master' into irp_rna_metrics
0bc4cbe Add missing thread parameter for bvatools_depth_of_coverage.
221eaae BFXDEV-339 Use rrna file in rnaseqc
8e95c99 BFXDEV-339 Use rrna file as ribosomal annotation (instead of ncrna)
5efa104 BFXDEV-338 New Nanuq MPS run association
7aab26f BFXDEV-338 New Nanuq MPS run association
6e6de07 BFXDEV-338 Add run_id in all commands available parameters
[email protected] [email protected] 1 commits
559973d correction other_options
2.1.0 Wed Feb 4 14:40:16 2015 -0500 123 commits
Francois Lefebvre [email protected] 2 commits
eefcc47 Added qualimap installa script + updated population
d9397b0 Changes to sailfisj , R install scripts
Joël Fillon [email protected] 104 commits
09344ee Version bump to 2.1.0
b3e8561 Changed procs= to nodes=1:ppn= in rnaseq and rnaseq de novo guillimin config
a63500d Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
a195837 Added libgd in PacBio mammouth config
a863cdd Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
e13ac41 Added pacbio_assembly.mammouth.ini + removed unnecessary wgs module
1cb2ea5 Added pacbio_assembly.guillimin.ini + adjusted guillimin cluster settings
b9f1264 README.md edited online with Bitbucket
ff58b26 Removed 'daemon' from scheduler options
2d4459d BFXDEV-292 Removed optional trimming dependencies for report in chipseq pipeline
6b9cdad Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
f40f39a BFXDEV-292 Fix metrics and report dependencies in chipseq pipeline
c1fb324 README.md edited online with Bitbucket
d8ade06 Removed tmp_dir validation since some directories are available on exec nodes but not on login nodes
44c931e Removed memtime from PacBio pipeline + updated smrtanalysis to version 2.3.0 patch 2
698d3f7 BFXDEV-292 Added cleaning in chipseq pipeline
cac6305 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
086ee05 Updated smrtanalysis module 2.3.0 with patch 2
0c6d970 README.md edited online with Bitbucket
f808abe Updated ChIP-Seq README + main READMEs
e789ffd Added BiSNP module install script
26a0629 Update mugqic_tools to 2.0.3 in rnaseq config
7af099d Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
d10a058 BFXDEV-292 Fix metrics tmp file preventing job to be up to date + module ImageMagick to use convert command on mammouth
367f86e Removed '\' before /ltmp/fillon in mammouth config files
0c1988f Added picard tmp_dir type validation
cf82065 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines into chipseq
0884bf5 BFXDEV-292 Added config files for all clusters in chipseq pipeline
2a57215 Updated mugqic_tools install to version 2.0.3
387c225 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines into chipseq
5017938 BFXDEV-292 Last steps implementation in chipseq pipeline
52d1f78 BFXDEV-292 Added UCSC genomes hg19, mm9, mm10, rn5
751e701 BFXDEV-319 Adjusted cluster settings in rnaseq.mammouth.ini + .ini absolute path for report
edc2651 BFXDEV-35 Standardized memtime module install
90f4aa5 Minor update in README-release.txt
ab65f5d Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines into chipseq
f37bed0 BFXDEV-292 Set peak annotation with internal homer genome in chipseq pipeline (incomplete)
9b35602 BFXDEV-35 Moved wgs-assembler module install in dev
77859cc BFXDEV-35 Standardized vcftool module install
a07ea0b Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines into chipseq
2ee4315 BFXDEV-35 Standardized ucsc module install
284138b BFXDEV-35 Standardized trinotate module install
9f31173 BFXDEV-35 Standardized trimmomatic module install
1fab82a BFXDEV-35 Standardized tophat module install
00b9355 BFXDEV-35 Standardized tmhmm module install
2917504 BFXDEV-35 Standardized tabix module install
6c1ec5b BFXDEV-35 Standardized star module install
5554746 BFXDEV-35 Standardized snpEff module install
25f53a1 BFXDEV-35 Fix smrtanalysis archive exec permission
275894f BFXDEV-35 Standardized smrtanalysis module install
6f3b27a BFXDEV-35 Standardized signalp module install
a335bfa BFXDEV-35 Standardized samtools module install
7cfda90 BFXDEV-319 Added rnaseq.mammouth.ini
dac40de BFXDEV-319 Removed java option -Dsamjdk.use_async_io=true in all .ini files
e394bf7 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines into chipseq
705f2c6 BFXDEV-292 Adjusted cluster settings in chipseq pipeline
a87203d README.md edited online with Bitbucket
2524cb9 README.md edited online with Bitbucket
af39fb4 README.md edited online with Bitbucket
e180a83 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines into chipseq
0daae6e Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
93c1a28 Fixed bam sub arguments in dnaseq bwa_mem_picard_sort_sam
934b42f Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines into chipseq
a5931e4 BFXDEV-35 Standardized rsem module install
dbaebd1 Moved repeatmasker module install script in dev
0c30ff4 BFXDEV-292 Minor docstring change in chipseq pipeline
dc0b988 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines into chipseq
ef6c09e BFXDEV-292 Added GTF for homer_annotate_peaks in chipseq pipeline
26894dc README.md edited online with Bitbucket
c7cdd1a Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines into chipseq
4f0b085 BFXDEV-292 Fixed input/output files bugs in chipseq pipeline
4c1cf7d BFXDEV-35 Standardized weblogo module install
bf36cc0 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines into chipseq
7952a5f BFXDEV-292 homer_find_motifs_genome and annotation_graphs steps in chipseq pipeline
b29cb3d BFXDEV-35 Standardized rnaseqc module install
05208ed BFXDEV-35 Standardized rnammer module install
e33776a BFXDEV-35 Standardized more prinseq-lite module install
fcc8bc9 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
d15d9b0 BFXDEV-35 Minor fix in AMOS module
07bba1e BFXDEV-35 Fixed path bugs in MUMmer and AMOS module install
99363ee BFXDEV-35 Standardized MUMmer module install
423c3c7 BFXDEV-35 Minor fix in module install template
c00bdfc BFXDEV-35 Standardized java module install
d185a50 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines into chipseq
8bed5d9 BFXDEV-292 homer_annotate_peaks step in chipseq pipeline
0bca196 BFXDEV-35 Standardized igvtools module install
1581fc9 BFXDEV-35 Standardized hmmer module install
2acdc49 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines into chipseq
cddbce7 BFXDEV-292 More macs callpeak in chipseq pipeline
ed7cf4e Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
b2d02b1 Fixed macs2 with generic shebang
cf61d7e Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines into chipseq
bbe5703 BFXDEV-292 Fixed missing samtools module for MACS2
ff1a4ec Standardized gnuplot module install
dcdc211 Standardized exonerate module install
5c47746 Minor change in README-release.txt
076c02b Version bump to 2.1.0-beta
953894c Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines into chipseq
1090d38 More chipseq deelopment
0841b02 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines into chipseq
ace0e30 BFXDEV-292 Beginning of macs2_callpeak step in chipseq
b404e22 Added qc_plots_R step in chipseq
43e70dc Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines into chipseq
51f3444 BFXDEV-292 First draft of chipseq pipeline
lletourn [email protected] 3 commits
9f9f60c Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
d2d65f0 BFXDEV-327 Used only one thread for haplotypecaller because of a race condition
639f650 BFXDEV-327 Used only one thread for haplotypecaller because of a race condition
Mathieu Bourgey [email protected] 4 commits
12ff20e Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
233244b RNAseq - correct stdin input issue of htseq-count - BFXDEV-318
fa33528 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
47c4cc8 RNAseq - htse-count: pipe samtools view -F 4 output in htseq-count instead of using the bam to remove error due to unmapped reads - BFXDEV-318
mathieu bourgey [email protected] 2 commits
7ec0344 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
1905eb6 COMMON - add fastq2 = None in sam_to_fastq pipeline step wehen the read are single - BFXDEV-321
mmichaud [email protected] 8 commits
953de3d BFXDEV-332 Fix depth_of_coverage 'other_options' by removing extra quotes
abca180 BFXDEV-332 Base the jobs configuration on the perl pipeline
619c076 BFXDEV-329 Add run and lane number to the alignment and metrics jobs name
6f4440f BFXDEV-202 Increase RAM for barcode counting
eac645f BFXDEV-328 Increase mem walltime to 48h (and set ram for SortSam)
ccb73f3 BFXDEV-331 Run Processing: Use a RG id that is unique across multiple lanes
c2218da BFXDEV-317 Run processing: Use the old name for the coverage and onTarget metrics
11ec9e7 BFXDEV-316 Fix errors when using a custom Illumina sheet file
2.0.2 Mon Jan 12 16:56:16 2015 -0500 80 commits
Joël Fillon [email protected] 54 commits
104778a Version bump to 2.0.2
bbdf438 Version bump to 2.0.2
9d984ce Fixed cluster resources in rnaseq_denovo_assembly.mammouth.ini
ee96fe3 Minor fix in pacbio_tools_split_reads config section name
8831a3a Even more standardization of module install
a2c5824 More standardization of module install
2b334e0 Standardized mugqic_pipelines module install
395d3ec Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
66230bd Standardized mugqic_tools module install
d9a56ab Standardized trinity module install
0549be9 Standardized cufflinks module install
ddbd8f2 Standardized MACS2 module install
386921e Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
9ba8d39 Standardized picard module install
55a5ccb Standardized cd-hit module install
d693b9a Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
9f05fe1 BFXDEV-310 Updated picard to version 1.123
a118e0d Standardized bwa module install
4dc7bb7 Updated bvatools to version 1.4 for dnaseq and puure
cca258b Standardized bvatools module install
94910f9 Standardized bowtie2 module install
3e8f201 Standardized bowtie module install
1b70a25 In picard_sam_to_fastq, updated skip test if FASTQ column present and BAM missing
345909a BFXDEV-290 Added job_input_files, job_output_files in JSON export
f6e623e Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
39e9ebf More JSON export for Daemon Scheduler
7295671 Standardized blast module install
947111a Standardized bedtools module install
9325049 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
c52d277 Standardized GATK module install
a69bd82 More module install generalization; first test with prinseq-lite
d116ebd Minor wget output file fix in prinseq-lite.sh and module install template
c30ad66 Added prinseq-lite module install script
b2059f5 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
8ca9017 Fixed pb wget --spider in install_genome.sh + various up-to-date checks in Homo sapiens assemblies install
21e59af BFXDEV-284 In nanuq2mugqic_pipelines.py, use native httplib, retrieve BED files and create adapters file
e9620ff BFXDEV-290 First draft of daemon scheduler
b778e5d BFXDEV-74 Finished cleaning in rnaseq denovo assmbly pipeline
a171581 BFXDEV-74 Started cleaning in rnaseq denovo assmbly pipeline
c1cee29 Reorganised lib functions more compact
1cc8e33 BFXDEV-74 Added cleaning in rnaseq pipeline
13475e2 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
84954f3 BFXDEV-74 Added cleaning for dnaseq pipeline + reformatted various bfx modules
1948d9d README.md edited online with Bitbucket
848a0ab Fixed bug use lstat instead of stat to check job up-to-date status without following symlinks
fdfcbdd Minor aesthetic updates on pipelines doctrings + README.md
da66a41 Generated pipelines README.md from docstrings using --help
89718b0 Added steps docstrings in RNA-Seq De Novo Assembly Pipeline
ab5e595 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
232bed5 BFXDEV-296 Added steps docstring for RNA-Seq pipeline
8d6f9a0 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
b665c4c Minor release doc update
bf9afb6 Update mugqic_pipelines module to 2.0.1
530edcf Version bump to 2.1.0-beta
lletourn [email protected] 1 commits
ccb812e Fixed picard installer, reverted back to 123
Mathieu Bourgey [email protected] 8 commits
fcd7134 pull before pushing Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
05b352d PacbioQC - Fix code vs ini section name - BFXDEV-315
d085269 RNAseq - correct discrepency in hsteq_count ini calls - link to BFXDEV-312
6773ef7 pull before pushing
d5d82f0 RNAseq - correct errounous section header in ini files - BFXDEV-312
98a456a Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
fdd92aa RNAseq -update guillimin cluster ini file - BFXDEV-307
b4a12a5 RNAseq - fix report dependencies - BFXDEV-306
mathieu bourgey [email protected] 9 commits
693ea1d PacBIo - add input files to the first pacBio job file (cp job) - BFXDEV-305
ce7f0b3 Revert "PacBIo - use the readset file as fisrt input file (cp job) - BFXDEV-305"
fc6eb26 PacBIo - use the readset file as fisrt input file (cp job) - BFXDEV-305
162af5e Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
2ff273b RNAseq - modify docstrings - BFXDEV-303
c58b6d3 DNAseq - correct report dependency (typo) - BFXDEV-304
ab81bc3 DNAseq - correct report dependency - BFXDEV-304
12830d3 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
b6f4e8f PacBio de novo - to allows running multiples sampes in parralele in the same analysis - BFXDEV-301
mmichaud [email protected] 8 commits
c14a281 BFXDEV-314 Illumina Run Processing: Output nanuq friendly metrics files
3141ccc BFXDEV-313 Run processing: Don't depend on the start fastq notification
5956b71 BFXDEV-310 Use Picard 1.123 with a bug fix in MarkDuplicate
d018879 BFXDEV-308 Fix wrong index in file name when the index is truncated in the sample sheet
793e91c BFXDEV-308 Fix wrong index in file name when the index is truncated in the sample sheet
000d043 BFXDEV-309 Use the hiseq qos by default on abacus
91cfb26 Run processing: Check the library type when the library source is 'library' to determine if the sample is from RNA
94f196e Run processing: Fix configuration for miseq (copy's destination folder)
2.0.1 Wed Dec 17 09:56:23 2014 -0500 33 commits
Francois Lefebvre [email protected] 3 commits
76a44bc Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
fe96c58 no message
0f6a3ec Modified R_Bioconductor script to accommodate older gcc's
Joël Fillon [email protected] 22 commits
bc72fc8 Version bump to 2.0.1
5868b85 Updated mugqic_R_packages to 1.0.1 and mugqic_tools to 2.0.2
3230102 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
fd49fed Updated /mugqic_tools.sh to 2.0.2
2b979a2 Fixed dnaseq species_vcf_format_descriptor with absolute path (no /sb/programs/analyste)
51fef9a BFXDEV-299 Fixed bug GATK realign with unmapped parameter not skipping other chromosomes
6890d45 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
9a53a11 BFXDEV-296 Added DNA-Seq step docstring documentation
a820bbc Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
4475a6b BFXDEV-296 Added detailed --help option with output in markdown format
cb49e7b Added detailed --help option with output in markdown format
bf7bb0a More PacBio README.md update
cd04651 README.md edited online with Bitbucket
93e28c7 README.md edited online with Bitbucket
48619e0 README.md edited online with Bitbucket
2e79a55 README.md edited online with Bitbucket
3a17272 PacBio Assembly README.md generated by --help
93e8124 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
69073ee Trinity + normalization settings for guillimin in rnaseq_denovo_assembly pipeline
8d8571f BFXDEV-26 Added cluster_max_jobs param in config files + added warning in PBS scheduler if this limit is reached
14194c6 Minor update in README-release.txt
38f24d7 Version bump to 2.1.0-beta
mmichaud [email protected] 8 commits
c661248 Run processing: Copy the rnaseqc metrics file to the bam directory to be compatible with nanuq
e9ecd7a BFXDEV-165 Add missing Perl module for bcltoFastq
44c06a0 BFXDEV-296 Changes to run processing documentation to use the generic help
ecb2447 Run processing: Put rnaseqc results in a specific folder by librairy
336a265 Run processing config: Only send email on abort and increase cluster wall-time to 48h for the fastq job
3e8733a Run processing: Add symbolic link to STAR created bam to fix output file check on re-run. The original file is renammed to follow nanuq naming conventions
7e8dddb Run processing: Fix rnaseqc sample list
7e38acf BFXDEV-297 Add RNA-SeQC in run processing pipeline
2.0.0 Thu Dec 11 18:12:54 2014 -0500 669 commits
Eric Audemard [email protected] 1 commits
dc40fe2 update mammouth .ini
Eric Audemard [email protected] 1 commits
62e2464 fix bug to find lib in pipeline python
Eric Audemard [email protected] 1 commits
02b7ea6 fixe bug on puure before Ray execution
Eric Audemard [email protected] 2 commits
3165f9a Merge branch 'python' of https://bitbucket.org/mugqic/mugqic_pipeline into python
bbe9d01 Bug fixed. Pipeline tested and validated on guillimin (step 1 to 21)
Eric Audemard [email protected] 2 commits
cd0dfbc Merge branch 'python' of https://bitbucket.org/mugqic/mugqic_pipeline into python
ad3c17e bug fixed : 1) unmapped read in realign 2) small script error in puure
eric audemard <eaudemar@imac6-ub.(none)> 15 commits
3b2258d bug puure
c0acd51 bug puure
0a33731 bug puure
c4ca954 update base.ini for guillimin
b47c7c9 add base.ini for guillimin
ab7535a 3nd script of PUURe done + some bug
5e7c1fe Merge branch 'python' of bitbucket.org:mugqic/mugqic_pipeline into python
a0b5418 2nd script of PUURe done + some bug
9576d84 add file for puure pipeline
844021a bug correction on 1st script of PUURe
c49f558 first script of PUURe done
8979304 add art software (http://www.niehs.nih.gov/research/resources/software/biostatistics/art/) : Simulation Tools add perl lib path for SVDetect
315bfc1 Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_resources
2b250c7 add script for install: SVMerge, RetroSeq, TIGRA, cmake
f89034f add biopython
[email protected] [email protected] 4 commits
caa90df add ini files. bug fixed on mkdir cov directory
4771482 add ini files
46f547e debuging step: fixe some bug
00d5fb8 bug fixed on puure + add all output in dnaseq metrics (gatk, picard)
Francois Lefebvre [email protected] 1 commits
e84abf3 picard version 1.125 module
François Lefebvre [email protected] 3 commits
4ae7aff tophat and bowtie2 according to template install script
35e4743 Minor changes to deploy script
cc01370 no message
Francois Lefebvre [email protected] 54 commits
22fd75c Updated R install scripts to reflect mugqic_pipelineS new name and deprecation of mugqic_resources
ccb88f5 fix to deploy script
3e061c3 update R packages list in resources
22d0545 Fixed bug when -v is specified
cd63425 more cleanup
a3e5bbe more cleanup
2be18df no message
8536bf3 Fixed bug in prefix mecanism
2e83482 Fixed default behaviour of update mode
2bb2812 R_Bioconductor.sh: update mode is default
7b04a5f First commit of the new R install scripts
6e908ac STAR install script update to 2.4.0e, accounting for new folder structure in the archive (bin/,source/, etc)
39922d9 shortStack install script
b032d1d tcltk is part of base install
c80bb97 Updated star install dev script
46888c0 magittr and other packages added to install list
d8773a3 Guillimin before mammouth
b819fb6 cufflinks version change
a62b519 Updated dependencies list (gqMicroarrays)
0a5aeba Added sailfish module install script
dfb486d bowtie 2.2.2
97999d4 minor changes to top hat and vienna install script
00d65aa Newer org.MeSH.* packages are too numerous and their installation take forever. Excluding them from the org.* packages list.
7d51b6a Created gmap-gsnap install script (dev)
af8b6c0 Added HTSFilter to del list
21cc201 more package dependencies
f34a34d Fixes to Trinotate related install scripts
b937e6f Removed G phase1 from R deploy script
8ae1b01 Multiple install scripts related to trinotate
d3a8fe2 module install script for BEERS, RNA-seq Illlumina reads simulator
7aca566 no message
ba527a2 GCC module call for phase1 only: before compilation and called by R module for run time.
915b729 modified example R.sh calls; need sh -l for module call to work on guillimin phase 1 ....
2402dee bash synthax fix
34d5126 entrezdirect installation script
2de4f30 Added -p option to R.sh: name of an env variable that specifies a prefix to -i and -m.
ba1638a no message
9903c2a cron modified, next clip module
c071c1e no message
6c8c26f Nextclip install script
99a9084 wrong file name in cron script
c4ed552 no message
d21308e temporary commits.. sourcing from Dropbox because problems with abacus
42a0781 Cleaning and and chomping module files too
21ef6d8 Changed chmod commands
0e7cacb Problem with roxygen2 on CRAN. install.packages does not find it for R<3.0.2. Msg posted to r-help. R.sh will not roxygenize until this is fixed.
67164c5 Last commit to R install scripts. Three files added: - R.sh is the workhorse which checks installs R/Bioc if necessary and performs updates. List of dependencies is hard-coded within this script. By default it will install/update the latest R version to $MUGQIC_INSTALL_HOME_DEV, hacking build.R to insure any subsequent package installation is performed with umask 0002. It can also install specifyc versions with -v, install to a specific location with -i and create the module file at a specific location with -m. The -f option forces rm -rf on any previous installation. The latest R version number is obtained by parsing the VERISON file from a R-latest.tar.gz download.
3c6a6c6 tar is silent, chmod done outside R
baacdad Combined installation/update in one script. package list and old install script will be removed in later commits
d186f78 Added R/Bioc Update script
453fdbd added varscan install script
8a2f543 Updated R install script
a3a16f3 list of R packages deps now linking to mugqic_ressources
22b0242 no message
Joël Fillon [email protected] 363 commits
bd175de Updated README-release.txt with more info
21cbf65 Version bump to 2.0.0
c3aea54 Added utils/ to PATH in module mugqic_pipelines
ae6ae81 Updated module mugqic_R_packages to version 1.0.0
b91ac7b Standardized mugqic_pipelines module install script
493da6e Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
6eb4df2 Updated PacBio pipeline steps as docstrings
2ebef9d Updated module mugqic_tools to version 2.0.1
718961a Fixed bug metrics.matrix sort tmpMatrix.txt before join
ab9e001 Fixed bug Picard sort_sam: add BAM index as output file only if sort_order='coordinate'
6610814 Added trimmomatic adapters FASTA files in bfx
975beb6 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
01f101c Minor update in rnaseq de novo pipeline
4b11101 README.md edited online with Bitbucket
d5b5827 README.md edited online with Bitbucket
e897da5 Updated SnpEff to 3.6 and snpeff_genome=GRCh37.75 by default in dnaseq pipeline
078f739 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipelines
d0e8ec0 Separate bed2interval_list job from picard.calculate_hs_metrics in dnaseq pipeline
347f888 Updated mugqic/tools/... to mugqic/mugqic_tools/... in config files
5b93fc3 Updated and standardized module install mugqic_tools-2.0.0
b7626d2 README.md edited online with Bitbucket
fd69eeb Renamed mugqic_pipeline into mugqic_pipelines
36aed54 Merge branch 'python' of bitbucket.org:mugqic/mugqic_pipeline into python
66a477b Added multiple input files for star step in rnaseq
35ac8b0 Added star memory/cpu settings in rnaseq.batch.ini
9990a91 Minor output changes in star.py
dc44a1d Merge branch 'python' of bitbucket.org:mugqic/mugqic_pipeline into python
f7667c9 Added step multiple candidate input file support + updated trimmomatic and dnaseq bwa_mem_sort_sam, picard_merge_sam_files accordingly
a6dda26 Added BAM index file as output of Picard merge_sam_files and sort_sam
8c3c87f Removed unused trimmomatic skip option
bc4bf73 Adjusted picard_merge_sam_files ppn value in dnaseq.guillimin.ini
11c164c Added symlink to BAM index (*.bai) in nanuq2mugqic_pipelines.py
ae0a63f Merge branch 'python' of bitbucket.org:mugqic/mugqic_pipeline into python
6cca375 Fixed BED Files split bug in nanuq2mugqic_pipelines.py
5edef09 Merge branch 'python' of bitbucket.org:mugqic/mugqic_pipeline into python
98f2dd8 Updated dnaseq dbNSFP2.0.txt to dbNSFP2.4.txt.gz
a5926c5 Replaced dnaseq dbsnp and known_sites parameters by known_variants + updated genome config .ini files with dbsnp_version + minor fixes
11f6245 Added vcf.gz.tbi in genome install
4cf7e43 Added log_report.pl and nanuq2mugqic_pipelines.py
86167d7 Reverted to previous pacbio_assembly name
fd9fd0f README.md edited online with Bitbucket
3e0de92 Added RNA-Seq report step (needs update for cuffdiff section)
165073d Removed differential_expression.goseq for cuffdiff and added self.gq_seq_utils_exploratory_analysis_rnaseq jobs in RNA-Seq pipeline
3ea16d3 Merged in jfillon/readmemd-edited-online-with-bitbucket-1417115922753 (pull request #6)
7dbb188 README.md edited online with Bitbucket
8c70917 Merge branch 'python' of bitbucket.org:mugqic/mugqic_pipeline into python
a3f02c3 Recovered previous gq_seq_utils_exploratory_rnaseq modifs
11863cb Merge branch 'python' of bitbucket.org:mugqic/mugqic_pipeline into python
62964d7 Update rnaseq_denovo_assembly.guillimin.ini with generic metaq, proc, pmem cluster settings
29a8087 Upgraded smrtanalysis module 2.3.0 with patch 1
08552cb Merge branch 'python' of bitbucket.org:mugqic/mugqic_pipeline into python
f604b0f Recovered rnaseq.base.ini with new differential_expression and goseq settings
6fb2716 Updated all R modules with mugqic/R_Bioconductor/3.1.2_3.0 and mugqic/mugqic_R_packages/0.1 if necessary
4bca911 Fixed merge conflict
8aab691 Added exploratory rnaseq step (partial)
fe1bcae Added genes file in rnaseq config
1101652 Updated Star module to 2.4.0f1
f64a60c README.md edited online with Bitbucket
9c0818a README.md edited online with Bitbucket
c0fc855 README.md edited online with Bitbucket
45c78c0 Merged in jfillon/readmemd-edited-online-with-bitbucket-1416841132369 (pull request #5)
a7dfa97 README.md edited online with Bitbucket
6583d2f Completed implementation of cleaning feature
cb4c0c6 Merge branch 'python' of bitbucket.org:mugqic/mugqic_pipeline into python
54378d5 More on pipeline cleaning feature
8113c51 Fixed merge conflicts + first implementation of pipeline cleaning feature
8c3c120 First implementation of exploratory step in rnaseq pipeline
4ccebd1 Merge branch 'python' of bitbucket.org:mugqic/mugqic_pipeline into python
9c33f31 Added Gene Ontology files in genomes + added goseq in rnaseq pipeline
5b2a7a9 First attempt to install genome Gene Ontologies annotations
1a34018 Fixed bug forgot super() call in Illumina and PacBioAssembly pipelines
a46d772 Updated all config base.ini with module_mugqic_tools=mugqic/tools/1.10.5
97243c7 Tagged mugqic_tools 1.10.5
10f05ae README.md edited online with Bitbucket
d624f80 README.md edited online with Bitbucket
b52b592 Added design file description + minor changes in README.md
c79b9c9 Updated rnaseq_denovo_assembly differential expression cluster settings
e8d968c Updated rnammer cluster resources
b882786 Merge branch 'python' of bitbucket.org:mugqic/mugqic_pipeline into python
e703a73 Added Python interpreter version check
9fb0472 README.md edited online with Bitbucket
fe5d954 Updated ini files with RAP_ID comment and rnammer settings
6fd646d Removed openmpi settings on abacus
1486f61 Design parsing support for empty or '0' fields
171bf2c Removed command dump in .done file due to bug
f4226eb Renamed readset and design file 'SampleID' column into 'Sample'
74bef6d Updated cluster queue settings for rnammer_transcriptome in rnaseq_denovo_transcriptome
a8ba35e Fixed version _argparser bug
f9796a5 Dumped command in .done file + moved version in MUGQICPipeline
a3d02bb Added differential_expression in RnaSeq pipeline
3873197 Fixed syntax errors in rnaseq
b0494b9 Added readset path normalization and variable expansion in readset file parsing
531b02b Fixed PacBio readset parsing bug
f17853b Added guillimin config file for rnaseq_denovo_assembly pipeline
bf1e01f Moved genome_configs into resources/genomes/config; updated README.md accordingly.
7eb3ada Imported mugqic_resources repository as 'resources' subtree
be12079 In PacBio summarizePolishing, removed redundant cmph5 sort and used a copy of cmph5 file to prevent Job from being always out of date
a3cf844 Updated PacBio pipeline with smrtanalysis 2.3.0
76f9f33 Improved Job debug log
d658c84 Minor cosmetics changes in README.md and PacBio readset file
7ce1851 Added Bitbucket URL in command line help
aab8a99 README.md edited online with Bitbucket
0c66e6f Added pipelines/pacbio_assembly/README.md; removed pipelines/pacbio_assembly/README.txt
49b0f0c Added
48eb836 README.md edited online with Bitbucket
e0ad931 Added pipelines/rnaseq/README.md
329a627 README.md edited online with Bitbucket
744fe94 Added pipelines/dnaseq/README.md
e76ca73 README.md edited online with Bitbucket
3426e21 README.md edited online with Bitbucket
0e4226f README.md edited online with Bitbucket
24a3bf3 README.md edited online with Bitbucket
415922f README.md edited online with Bitbucket
8bd144e README.md edited online with Bitbucket
34db02a README.md edited online with Bitbucket
44024ca README.md edited online with Bitbucket
a8a0227 README.md edited online with Bitbucket
0d57ec0 README.md edited online with Bitbucket
f6bb2f4 README.md edited online with Bitbucket
5442dec README.md edited online with Bitbucket
d738c55 README.md edited online with Bitbucket
73a1d8c README.md edited online with Bitbucket
47ae71c More on README.md
0ae6c2d README.md edited online with Bitbucket
9a9751d More general documentation on pipelines
cce8833 Replaced internal RAP ID with generic variable in dnaseq.[guillimin|mammouth].ini
49f5e04 Updated igv_genome config param to match generic <genome>.fa.fai index + updated all genome configs with Ensembl 77
bd09fa8 Module versions update in config files
ace8e6f Fixed pacbio filtering dependency bug
c971597 Minor comment update in homer module install
0ba8de7 Changed DnaSeq snpeff_genome to hg19
8abed9c Fixed bug readset.fastq[12] attributes should be writable
dd78287 Reverted SMRT Analysis module install script to version 2.3.0
9a34f43 Added SMRT Analysis 2.2.0.133377-patch-3 in module install script
68c77e5 Update SMRT Analysis module instal with 2.3.0 patch 0
b06999f Fixed dbSNP download_path bug
4612110 Updated dbSNP to build 142 for Homo sapiens genomes GRCh37 and GRCh38
b8e26ad In genomes/install_genome.sh, added functions skipping if up to date + added rRNA FASTA creation and BWA indexing if present in ncRNA fasta
49c8cf3 Moved star_index/ into genome/
e0fe746 Added install_all_genomes.sh ; fix STAR module version for index creation
7e92a39 Added STAR index
d67a0c4 Added version number + updated README.md (incomplete)
515ab99 Added star module install script
39d4b84 Updated gqSeqUtils report calls and parameters
162ec0b Fixed merged conflicts
93a94e9 Updated RNAseq nozzle reports with Python version
e4bae26 Updated DNAseq nozzle reports with Python version
5ad7b16 Renamed bio module into bfx
ad6c8b1 Added config file list support in gq_seq_utils report and pacbio_assembly
83cd491 Added report and compile steps in pacBioAssembly pipeline
59fafec Added log.debug for job.is_up2date + set config.filepath with config.trace.ini file
c90118a Added raise NotImplementedError for PUUre and RRNATagger pipelines
4702215 Updated config genome paths with new genome files organization
13471eb Fixed bug smrtanalysis.reference_uploader transforms '-' into '_' in fasta filename
1d948bc Moved /sb/programs/analyste/genomes/blast_db/README.txt on bitbucket genomes/blast.sh + move oryCun2.sh in genomes/old/
46062c5 Updated default dnaseq genome paths + readset library, run, lane and config sequencing_center are optional for dnaseq bwa mem
45ec207 Fixed permissions bug for Homo sapiens genomes install
eb7ea9c Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
d052f61 RELEASE -> VERSION; DBSNP from NCBI for Homo sapiens; symlink DBSNP to Ensembl VCF for other species
f103474 Added pacbio mummer step
f2e84d7 Added pacbio steps up to blast
29af2de Added job input/output files debug in pipeline
3ae18d9 Fix cluster settings from job name instead of step name
1da5b28 Fixed pacbio pbutgcns cmd missing &&
412287e Check job input/output files as valid paths instead of regular files
a072760 Update genome installs with Ensembl release 77
a38bdfd Fixed rnaseq cluster_submit_cmd_suffix bug
7e0c6e8 Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
799ccb4 Fixed permissions on genome files
7b1b697 Use Ensembl genome instead of 1000genome
c7dd349 RNASeqQC now uses GTF with transcript_id only
7aa6712 Removed abacus config .ini
b6689cc Updated ini files with proper genome keys
2e9c839 Added genome configs
802c39d More on pacBio assembly steps
49bdc5c Updated rnaseq genome config names
e91a300 Increased abacus cores and memory for insilico_read_normalization_readsets
59e7acc Added DBD::SQLite in perl install dependencies
3fae17c Added trimmomatic ram in config + added picard.sam_to_fastq VALIDATION_STRINGENCY=LENIENT
ca5b125 Added trimmomatic ram in config + added picard.sam_to_fastq VALIDATION_STRINGENCY=LENIENT
f551b41 Fixed trimmomatic headcrop length order + insilico_read_normalization_all job name
eeb1ff6 Merge branch 'python' of bitbucket.org:mugqic/mugqic_pipeline into python
37a1260 More pacbio steps + here-document for bash command to avoid escape characters in output
4cdd7a9 Added DBI and PDF::API2 as CPAN dependencies in Perl install
0c4d6cd Fix RSEM reference dependencies
59f01f9 Standardized perl module install with reduced CPAN dependencies
f51ae0d Minor trimmomatic thread update in rnaseq_denovo_assembly.base.ini
c3be9ab Added rnaseq_denovo_assembly.mammouth.ini + minor path fix
74e88c0 module_tools -> module_mugqic_tools + pacbio filtering step (incomplete)
1870e1a Added rat,dog,chicken genomes + python fix compiled in ucs4 + matplotlib manual install
3599716 Standardized chipSeq modules as separate weblogo, homer, macs install scripts
07f6d3b Tagged mugqic_tools 1.10.2
f29ef00 Various fixes in rnaseq + pacbio first draft
ea16a1d Removed picard_index and sam_index subdirectories + error tweak for gunzip human_g1k_v37.fasta.gz
2cb5f0b Added dnaseq alignment readset subdirectory + mugqic_log not sent if pipeline has no jobs
94590ba Cleaned genome_configs
17a3b31 Cleaned genome_configs
ec62c58 Minor documentation change
a62ab92 Removed old RRNATagger files
3d52780 Added MUGQIC parent pipeline with call_home log function
a409b72 Added config trace creation from merged input config files
178d1c1 Change readset file column name Sample -> SampleID; remove -V from qsub; updated gtf tophat index path in rnaseq
0b1bd44 Creation of the major model genomes with new standard organisation
8a6a093 Fixed puure.abacus.ini filename
dba20ba Merge branch 'python' of bitbucket.org:mugqic/mugqic_pipeline into python
cf3c3ba Fixed merge_and_call_gvcf output file name + updated dnaseq with mugqic/GenomeAnalysisTK/3.2-2
8614cd1 Updated rnaseq config files and parameters + minor dnaseq config update
ab1c6d1 Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
a1466e7 GENOME_INSTALL_TEMPLATE with Ensembl support
0b2880b Fixed mkdir metrics in illumina.py
66b529d Minor fix in dnaseq.batch.ini
e002351 Minor fix trinotate nb of columns + scheduler date formatting
bff0301 Merge branch 'python' of bitbucket.org:mugqic/mugqic_pipeline into python
bc2b9fc RNASeq De Novo pipeline implemented except nozzle report
23a4a72 Merge branch 'python' of bitbucket.org:mugqic/mugqic_pipeline into python
e621271 Fixed samtools_sort and baf_plot options for dnaseq on mammouth
4491132 Merge branch 'python' of bitbucket.org:mugqic/mugqic_pipeline into python
7b211be Merge branch 'python' of bitbucket.org:mugqic/mugqic_pipeline into python
c91f835 Added fastasplit in RNASeq De Novo pipeline
dc50442 Minor fix in dnaseq.mammouth.ini tmp_dir and R version
a6570ef Minor scheduler formatting
2a9c298 Merge branch 'python' of bitbucket.org:mugqic/mugqic_pipeline into python
edaf6f1 Added normalization steps in RNA-Seq De Novo pipeline + fixed python lib bug with absolute path
f88a448 Modified -j and -c options descriptions + removed all .pyc files
47a1c95 Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
95b82a3 Restandardized mugqic_tools install template
2ab7d2a Merge branch 'python' of bitbucket.org:mugqic/mugqic_pipeline into python
10f5ecc Added first draft of Puure pipeline
82006ac Added dnaseq mammouth config file
e4b99ee Added dnaseq guillimin config file
6f1cf24 More on GENOME_INSTALL_TEMPLATE.sh
5dc0690 First draft of GENOME_INSTALL_TEMPLATE.sh
4eb9823 Minor fix in Python module install
c950b25 Fixed python module install + minor fix in MODULE_INSTALL_TEMPLATE.sh
ddd1e5d Standardized python module install
8eede7f Moved AMOS module install in dev and standardized it
e2912e0 More config standardization
e22b5c4 Minor fix in ucsc module install
0c9abe7 Standardized UCSC module installation + minor template improvements
2873b94 Fixed merge conflicts in bio/rrna_amplicons.py
475e92c Reorganized all config parameters
b8d0673 Minor fixes
d609431 Merge branch 'python' of bitbucket.org:mugqic/mugqic_pipeline into python
d73fe49 Fixed minor tophat bugs + scheduler proper exit code
e19aaae Added rnaseq steps up to cufflinks
6cf0a06 Merge branch 'python' of bitbucket.org:mugqic/mugqic_pipeline into python
b65411f Added cufflinks module
104113f Added gtf in htseq + argparser factorisation in pipeline classes
8b68b09 Added bio/htseq.py
dd38967 Fixed newline and output file bugs in R mugqicPipelineReport + batch scheduler with job.done
96fcc8e Fixed merge conflict in samtools.py
631d37f First htseq draft in rnaseq + snv fix in dnaseq
655c6bb Added multiple ini files argument feature + first draft rnaseq raw_counts
7f92b49 Merge branch 'python' of bitbucket.org:mugqic/mugqic_pipeline into python
a351008 Added rnaseq wiggle step
3d3d844 Fixed input/output files bug in concat_jobs()
bdf6c8b Removed all .pyc from git
f6995a9 Added rnaseqc step in rnaseq + other minor fixes
cec67b7 Grouped common dnaseq and rnaseq features in a parent pipeline Illumina
192486b Fixed minor bugs
4441fb9 First rnaseq draft; dnaseq with os.path.join
443c9c9 Update input/output files for metrics_snv_graph and deliverable
f776268 Modified sys.path according to dir changes
710c0bd Reorganised directories
55e7904 All dnaseq steps implemented (need to test though)
7cde825 Added dnaseq steps: rawmpileup, rawmpileup_cat, snp_and_indel_bcf, merge_filter_bcf, filter_nstretches
af2c35a Added dnaseq steps merge_and_call_gvcf, dna_sample_metrics
b0ea4b8 Added dnaseq haplotype_caller step
952ebec Formatted batch scheduler + calculate_hs_metrics, callable_loci, extract_common_snp_freq, baf_plot steps
2a3b223 More dnaseq steps + job input files validation
dba5767 Moved python scripts in mugqic_pipeline directory
c941e47 Removed step loop + standardized step names
96e6e96 Added indel_realigner step + fixed job is_up2date with dependencies
6cedd33 Added first GATK functions + extended dnaseq pipeline
2c2937c Added first gatk draft + parse Nanuq readset file
397fb36 Added global config object + picard module
4dd79a1 Added group, pipe, concat job functions
fef73cd Added DnaSeq trim and mem + force option
24057c2 Torque scheduler test OK
b484d11 Added torque submit header
dc45f44 Added scheduler and log
b6fada2 Updated mugqic_tools install with version 1.10
16e9aa3 Added argument parsing and more
2e6cc0e First Python version with basic args parsing
3ee3e3e Core classes coded
97d8940 More on python prototype
fa8dd9a Added DB_File Perl module + minor permissions fix
a24fd3a Added prerequisite for modules rnammer and trinotate
e6d3ded Standardized trinotate and dependencies module install
af7cea5 Standardized BWA module install
53b9605 Moved R&D modules in dev/
fbccba1 Added archive check in MODULE_INSTALL_TEMPLATE.sh to avoid redundant archive download
1e72c28 Minor fix on template install: archive dir with /
8898ddf Restored blat module in dev
54192b2 Removed blat module (already part of ucsc module)
6a70836 Prefix java module by openjdk
d5575c0 Updated Java module install with OpenJDK
3e9546b Updated RSEM and Trinity module install with latest version
f80d0d2 First Python draft
65176a9 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into bam2fastq
28f5ab6 Fixed conflicts in merge master into bam2fastq branch
26c226a Resolved conflicts with master branch
1729a4a More on object-oriented dnaSeq pipeline
2378320 More on object-oriented design
a3dabbe More on object-oriented redesign
3d942d8 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into bam2fastq
455ebed More on object-oriented pipelines
20bc7af Minor variable name changes
b2c5d0f Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into bam2fastq
d017c57 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into bam2fastq
9b1ae90 Incomplete version of bam2fastq dnaseq pipeline
e87e5b9 Added Parse::Range in Perl modules
29bd3d9 Solved merging conflicts in rnaSeqDeNovo.mammouth.ini
a91dbdc First object-oriented version of RNA-Seq De Novo Pipeline
2255e9c Minor RSEM install script fix
a7c1275 Updated RSEM install script by modifyin Perl script shebangs with /usr/bin/env/perl
a37edd0 Updated mugqic_tools to version 1.8
063caa2 Added PerlIO::gzip as module dependency
2fa1750 Added dev/prod/ environment in MODULE_INSTALL_TEMPLATE.sh + modified all shebangs with bash
ae10289 Merged dnaSeq.pl conflict from master to bamToFastq
a6d0d76 More on bamToFastq process (uncomplete)
f911e8a Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into valid_param
89a3066 Merged master in local branch and resolved conflict
ced737e First bamToFastq attempt in dnaSeq.pl
338afbe Minor fix in snpEff archive name
8154c76 Standardized snpEff, VCFtools install scripts; added Java install script; added various permissions
17a4f95 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into valid_param
c351f09 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into valid_param
b64d2e7 Merged with master
27c29de Even more on bam2fastq
9c38e40 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into valid_param
04f66e4 More on bam2fastq
ca1172c Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into valid_param
e37f19a Some steps toward bam2fastq support
ab015b8 Standardized tophat and cufflinks module install script
201cc7d Standardized bowtie, exonerate, samtools module install scripts
bbc946e Fixed module directory named "pipeline" instead of "mugqic_pipeline"
25141fc Standardized mugqic_pipeline module install script
732d095 Added others permissions for MUMmer and wgs-assembler
493b28b Updated mugqic_tools version number to 1.6
689141b Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
ea2d0ae Installed trinity and rsem in production
9b4f23f Standardized Trimmomatic module install
ff81b27 Updated RSEM version, RSEM and Trinity permissions
e51836d Upgraded to mugqic_tools-1.5
f205a7a Added BLASTDB variable in blast module install script
b3f1686 Minor permission fix
9147435 Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
e894200 Updated Trinity module install with last version
819415a Updated mugqic_tools install script according to MODULE_INSTALL_TEMPLATE.sh
5093baf Renamed module install template
9473a90 Added read/execute permissions for others in module install template
0e6cf37 Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
99c14da Added ape + ctc R dependencies for Trinity differential expression analysis
f6648d9 Updated Trinity edgeR PATH
1f140b6 Removed comment in Trinity install script
0348f39 Updated trinity and rsem module install scripts in dev
5e0865f Moved some install script to dev/
91784d0 Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
29666f4 Clean up obsolete/dev install scripts
4ec387a Removed Makefile draft
90d94d3 Minor change
7711123 Initial import of genome and module install scripts from mugqic_pipeline repository to mugqic_resources repository
johanna_sandoval [email protected] 5 commits
9f787f3 Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
95ac9e3 BFXDEV-133 detected perl bug on homer and weblogo scripts using our own perl module, updated perl scripts shebangs
4b5a245 Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
72a19c1 BFXDEV-133 Adapt the software/module installation to guillimin phase2 requirements
90db5b5 BFXDEV-82 version 1.7 of mugqic tools, added bug correction for R-tools related to chipSEQ pipeline
[email protected] [email protected] 12 commits
0418260 Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
d33f8e2 prepend popoolation path to PERL5LIBS
c5a79a8 Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
05d6532 added Picard Mark duplicates no optical v 1.90 to the dev software repository
5edf0ed pmarquis: Added genome setup for arabidopsis thaliana-TAIR10
4bc9c17 Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
a8a9a0f added env-variable POPOOLATION_HOME to the module file
13c9b20 added an installation script + module for popoolation
f2046f1 Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
2c85b4f added plotrix to the list of R packages
eaab7c1 creating R v.3.0.2 module in dev
3a6476d installing R on the test environment
jtrembla [email protected] 24 commits
4d370a6 rrnatagger.py continuation
a228ba6 completed bio/rrna_amplicons.py
a4bbfc7 continued coding of rrna_amplicons.py.
f82ac52 writing rrnatagger pipeline in python. First step works.
cf40514 Added two functions (that actually works :-)). I need to convert the rest to python syntax.
bc82663 added rrna_amplicons
d045a6a renamed RRNATagger to rrnatagger
d0a7f34 Added rrnatagger.py and list of steps.
9f616ee added lib path.
b0d9af6 Added bamtools.
907ef6b Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
87e713a Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
e3ddbbb minor fixes.
058fa82 Updated bwa version.
6432b27 New module install scripts.
cecd97f Added path (prepend-env) to root/R-tools.
c61c904 Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
119c7ad minor modif to module list for perl.
2fe2654 Added comments to smrtanalysis installation (2.2.0). Tested and installed.
9858f66 Added muscle aligner.
9403ab7 Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources corrected typo, then merges..
ac2a43e corrected typo.
5c1e23a Added chmod at the end of the install module "scripts".
79e2d4a Added list/script to install modules. Could be improved...
Julien Tremblay [email protected] 1 commits
72347df added module DB_File to perl module installation.
Julien Tremblay [email protected] 6 commits
7d2d5a3 Added RRNATagger-tools to prepend path in the module file. BFXDEV-31
b792e6a added python install script.
1be6f84 Fixed two missing paths for PERL5LIB
0b26b2d Added perl to mugqic modules.
82b9d19 Modified install scripts according to our group's template.
3156d84 Added gnuplot-4.6.4 and memtime-1.3
lefebvrf [email protected] 1 commits
923d661 Removed genelenght.r. Use mugqic_tools/R-tools or gqSeqUtils directly with HERE docs or Rscript -e
lefebvrf [email protected] 14 commits
0be2b76 Removed superfluous (already in base) dependencies from list
4cf1272 violin plots package added to list of dependencees
16882a5 PerlIO::gzip is a dependency for Trinity clusterProfiler as R package
0530c57 Guillimin phase 2 added to daily R deploy
9a37c3c R.sh needed a module call to a more recent gcc than system one.
e90b9ca devtools::install_local() would install packages to home folder if exists... .libPaths(.Library) solves the problem
923b50a —vanilla removed from R.sh too
a13f582 blurb added related to last commit
d028e16 Add creation of Rprofile.site to R install script. This will force using cairo X11 backend since cairo is not always set to default when available…
321311b Added ViennaRNA and mirdeep2 install scripts
33dfb87 Small hack to tools::build.R when installing R allows umask 002 (!)
7496779 Corrected exit code, first version of R_deploy
b8db61a Additional setdif(reps) to avoid duplicate installations -> slow
2082c05 Fixed leading tabs problem in module file by using <<-EOF here tag. Neutralized R_LIBS to insure installation proceeds correctly when R module already loaded Added vanille biocLite() call
lletourn [email protected] 45 commits
e76f595 Merged old perl changed into python
0f7f0f8 Fixed haplotypeCaller output file name extension
4098ccc Version bump mugqic pipeline to 1.4
b9625ab Version bump to 1.5-beta
7e8d28c Bumped bowtie to 1.1.1
2528f92 BVATools version bump
277abf2 FastQC version 0.11.2
c1d9878 Version bumped Ray to 2.3.1, removed unneccessary fix now
45b85da PIcard Version bump to 1.118
9db0c54 Added pysam
fc0ea4c BWA version bump AND fixed the script, it was a bad merged script
cc5aa56 Updated GATK and mutect
2cd15d6 Merged diffs
b10f91e Added gsalib and added configure switch
cb1777f Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
3677916 Version bump pipeline to 1.3
58fff5f Force output file name
ef35a74 Version bump bvatools to 1.3
a441cda Version bump of mugqic_tools and snpeff
9b6fa74 Added ascat
a669439 BWA Version bump to 0.7.8
6109739 Added the jellyfish tool
6108922 Updated gatk
09e5270 Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
44e530a Added Mutect home
9a96cbf Version bump
6827d55 Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
adda765 Version bumped wgs-assembler, bwa, picard
674305d Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
9e6a4c6 Version bump bowtie2 bwa picard
287aa23 Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
c2aac9a Added aspera instructions
701df8c Version bumped vcftools to 0.1.11
6f5a6ed Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
c8f949a Version bumped blast to 2.2.29
d0dab7f Bumped version of picard
4e6fcc4 Updated snpeff
ff4f397 Version Bump of the pipeline
34c15b0 Added variable to access the repo's location
fa87e19 new Ray version
a6402ac Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
ac6513f Updated BVATools to 1.1
ea6aff9 Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
dca240f Added BVATools
71bfcf2 Added wgs assemble
Louis Letourneau [email protected] 1 commits
e1c5341 BFXDEV-246 Version bump
Mathieu Bourgey [email protected] 7 commits
14060c1 Remove conflicts in modules/mugqic_tools.sh and modules/dev/star_dev.sh
cb81397 update modules/mugqic_tools.sh to 1.10.4
b2db257 remove decrepated python module script and add a new one
16d3068 replace dev module in module/dev/ cufflinks_dev.sh star_dev.sh
fd6119e Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
85a4523 add genomes/oryCun2.sh modules/cufflinks_dev.sh modules/star_dev.sh
b35f6de up-date mugqic_tools.sh version to 1.7
mathieu bourgey [email protected] 47 commits
0eff10b Merge branch 'python' of bitbucket.org:mugqic/mugqic_pipeline into python
6272cb0 Python - RNAseq : allows more flexibity in fdr and p-value for goseq AND remove native goseq approach - BFXDEV-289
e78717a Merge branch 'python' of bitbucket.org:mugqic/mugqic_pipeline into python
8694d0c Merge branch 'python' of bitbucket.org:mugqic/mugqic_pipeline into python
218dbdc Python - RNAseq: update rnaseq.py
a133310 Python RNAseq - updates
6a061db Merge branch 'python' of bitbucket.org:mugqic/mugqic_pipeline into python
5e8df54 Python RNAseq - updates
61a12cf Merge branch 'python' of bitbucket.org:mugqic/mugqic_pipeline into python
b1f9bc8 change RNAseq python update
5c9e82f change RNAseq python cuffnorm output to include sample names
015fab6 remove RNAseq python step bug exploratory v2
582e5e3 remove RNAseq python step bug exploratory
b14fbf9 remove RNAseq python code conflict
62a0e4f PYTHON -RNASEQ: star, cufflinks, htseq updates
40970ff Merge branch 'python' of bitbucket.org:mugqic/mugqic_pipeline into python
e600a91 Python: RNA - update star + DGE anbd goseq input oputpuyt file correction
01fccf9 resolved pipelines/rnaseq/rnaseq.py confilcts
87f92a3 major RNA implementation: STAR, picard, cufflinks, etc...
a39a35e Python RNAseq: add cufflinks > 2.2.0 new workflow - cullinks - cuffmerge step done
d902b4d Python RNAseq : update STAR - add optional read sorting during alignment
8f572bc Merge branch 'python' of bitbucket.org:mugqic/mugqic_pipeline into python
8305fe7 Python - RNAseq: add STAR alignment 2 pass && add utils folder/function for methods generic unrelated to any software or tools
c713736 Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
4cd30e3 update samtoiols module install to 1.0
860eba6 python : RNAseq - change ini
a6ea523 On goinig adding star to RNAseq
33f80d6 add dnacopy in R.sh edited online with Bitbucket
3bdf7cb Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
0f1910e correct python.sh script that was not workin for the modules: BFXDEV-46
27348a0 Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
793e633 add specific RNAseq packages to R package list
1016ccd replace correct permissions in mugqic_tools - BFXDEV-55
fda2802 Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
40d5ef5 ngoing python module package
03dab09 update breakdancer module
7f60581 update breakdancer module
494455b pdate breakdancer module
9deedd9 change in samtools modules and add breakdancer module
02fde14 Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
bfdd544 add module igv
60e6732 Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
6615a3b create module install sh for the mugqic pipeline
30983a9 update nugqic_tools to the new version 1.2
834b58e Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
19f7508 update mugqic_tools
5e75b3d update modules/mugqic_tools to point to the new repository mugqic_tools with tag v1.0
mmichaud [email protected] 54 commits
4617cd8 Run processing: Remove duplicate '.' in dup bam file
f72f529 Run processing: Run blast on bam file, fallback on fastqs
ae2fcbd Run processing: Add the suffix '.sorted' in the readset bam name
7bb7a50 Run processing: Merge md5 jobs (fastq+bam) and run qc graphs on BAM (or fallback to fastq)
5603e88 Run processing: Run DepthOfCoverage even if there is no BED file
a81e719 Run processing: Use bcl2fastq 'force' option instead of removing destination folder
1890439 Run processing: Remove dependencies dependencies from copy job
6f33eaa Run Processing: Use a kind of factory to manage the different aligners
e006fa9 Run processing: Remove the dependency to samtools by using picard to generate the STAR BAM index.
f46022c Run processing: Move md5 step later, to optimize job allocation and to minimize condition when the md5 job is finished before the copy job is submitted
8d06973 Run processing: Remove unused adaptor columns parsing
fd4705a Run processing: More documentation (sample sheets)
60abc0c Run processing: Output the index metrics file in the output folder, not the run folder
88a0907 Run processing: Use xfer queue for downloading BED files
ba1b4d6 Run processing: Add samtools module version and increase number of core for STAR (a test job took 71G of ram)
3186121 Run processing: Manually generate BAM index file when using STAR.
1b42a02 Run processing: Fix usage in readme
f4e87a7 Run processing: Add documentation
a6e1838 Run processing: Add missing '.' in bam name
7aad80b Run processing: Fix copy step exclusion
7100d7c Run processing: Copy output file is now in the copy destination folder
073b8a9 Run processing: Change back to manual copy job depedencies gathering
ff84ee0 Run processing: Initial RNA-seq support with STAR
b5969a3 Run processing: Return empty list when there are no input for the copy job
b5b30a6 Run processing: Fix copy job inputs
58e4326 Run processing: Fix end copy notification job queue
43c153a Run processing: Fix qc output file
9d9e87a Run Processing: Fix race condition in HsMetrics interval file creation
7dc2b9b Run processing: Fix configuration for blast and qc
edb3269 Run processing: Generate sample sheet in the submit job method
f5f23ff Run processing: Fix config for index step, now using 'index' category
348972b Run processing: BAM metrics are run in markdup output
176e96f Run processing: Various fixes for the first test run
63944b9 Run processing: Various fixes for the first test run
1043bb1 Run processing: Various fixes for the first test run
c8ee9b0 Run processing: Add basic support for different aligners
aa16b2d Run processing: Get copy step dependencies by introspection
c74a06b Merge branch 'python' of https://bitbucket.org/mugqic/mugqic_pipeline into python
3af310b Run processing: Delete existing 'Unaligned' folder when running fastqs
583c80f Put Illumina configure bcl2fastq in a job
aa93387 Run processing: Use . as job name separator
ddafcfe Use $MUGQIC_INSTALL_HOME variable in config file to replace hardcoded paths
79d09cc Fix arguments for IlluminaRunProcessing by removing readset argument from MUGQICPipeline
cbe8ddc Run processing: Use run_dir instead of run_directory to follow output_dir convention.
aa213fe Run processing: Improvement to the sample sheet generator to loop only one time
7d16bcf Run processing: Seperate config files for MiSeq and HiSeq. The base config file still hold for a HiSeq
df783bc Merge branch 'python' of https://bitbucket.org/mugqic/mugqic_pipeline into python
2b53d11 Run processing: Add wget download of sample sheets and bed files. Fix Casava sample sheet generation.
07aacb6 Add some imports from __future__ to ease the transition to python 3
7af4b28 Add copy job dependencies
82841bf BFXDEV-283 Fix reference for coverage calculation, add copy step.
213e716 Change illumina_run_processing name to follow code conventions
8d8e1af Code convention changes
f51f5e0 First draft of the illumina run processing pipeline in python.
[email protected] [email protected] 1 commits
acde237 adding sh tools for riboRNA
[email protected] <pmarquis@abacus1.(none)> 1 commits
f6ddfbe BFXDEV-112 install genomes from IGENOMES
[email protected] [email protected] 1 commits
2fc3f9d usearch.sh
[email protected] <pmarquis@abacus2.(none)> 2 commits
481bc98 Merge branch 'master' of bitbucket.org:mugqic/mugqic_resources
7ff159c gene_length
1.4 Mon Nov 17 13:15:48 2014 -0500 139 commits
Francois Lefebvre [email protected] 2 commits
667c6f7 README.md edited online with Bitbucket
ee9efd5 README.md edited online with Bitbucket
Francois Lefebvre [email protected] 6 commits
3355905 Previous minor bug fix (dots in sample names) actually introduced major bug.
0bc3e58 temp files remove
93c2905 rnaseqc other options possible
c045541 rnaseq .ini file more tophat options. BFXDEV-215
8270318 Added --transcriptome-index support to tophatbowtie.pm, as well as possibility for other options.
0ef6afc Added --transcriptome-index support to tophatbowtie.pm, as well as possibility for other options.
Francois Lefebvre [email protected] 7 commits
242f2bc Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipeline
c004e51 Passing projectName to SubmitTocluster can create invalid job names. Replaced with string
e578fb4 variable name was inappropriate
eab0310 Updated rnaSeq mammouth template .ini file.
202215e Defined a job name prefix for wig zip. 'metrics' as a job name was not enough information
59f1528 cuffRescolumns and dgeRescolumns now in goseq param section. Also adjusted those values for UCSC genomes hg19 and mm10 templates, original value did not work.
524dd82 overwrite.sheets=TRUE to avoid common problem of updated projects
[email protected] [email protected] 4 commits
257c44d Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
4b8a23b patch3 applied; see BFXDEV-260
3c6e850 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
ff5fe3d change R module due to crashing nozzle report generation, see BFXDEV-255
Joël Fillon [email protected] 34 commits
0860442 Updated pacBio .ini config file with new smrtanalysis module name: 2.2.0.133377-patch-3
c2d5000 Updated config genome paths according to new genome organization
030e601 Updated chipSeq mammouth config with new Homer 4.7
be23877 Added explicit Python module in rnaseq cuffcompare step
9d16e5a Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
c256913 Added newline after mugqicLog command
8f3c5f3 Updated rnaSeq.mammouth_hg19.ini with generic /nfs3_ib/bourque-mp2.nfs/tank/nfs/bourque/nobackup/share/mugqic_prod path
1fd8a63 Removed explicit RAP ID in RNASeq De Novo config files
0efe22d Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
6aac202 Removed moduleVersion.htseq ini ini config files
ded1a46 Fixed missing java module in igvtools
2c37b3e Minor fix in dnaSeq step_range help
cf08611 Added default RAP ID in RNA-Seq De Novo guillimin config file
e67468a Added --exclude <fastq> option in illuminaRunProcessing rsync for samples having BAM files
98420e4 Uncommented phone home in dnaseq
0e6e8a8 BFXDEV-203 Create one .done with checksum instead of one per output file + update config files with default adapters path + update perlpods removing -e option
9886061 Fixed bug missing Library Source -> column not mandatory + updated pipelines/rnaseq/rnaSeq.guillimin.ini with accurate module versions
e07ffd8 README.md edited online with Bitbucket
d02ae67 Added comment to update Resource Allocation Project ID
13bf5c9 BFXDEV-221 Migrated abacus/guillimin config files from msub to qsub
d8a411e MUGQIC call home is now run inside bash script after job submissions instead of bash creation.
5c2627a Updated chipseq mammouth config with python 2.7.6
29163dd README.md edited online with Bitbucket
bad3648 Added call home feature notice in README.md
9413014 Fixed RNA-seq de novo resume jobs; added env variable WORK_DIR in pipeline; formatted bash output
b2f3fd5 Another glob fix for prefix path check in LoadConfig::getParam
65b9923 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
768184e Minor fix for config param prefix path
74d4328 Added prefixpath check type in LoadConfig::getParam
249a5cb Fixed transdecoder bug ln: creating symbolic link 'Trinity.fasta.transdecoder.pfam.dat.domtbl': File exists
59ea4b6 BFXDEV-32 Fixed wrong transdecoder file path for missing PFAM 'cds.' prefix
9c6fe6f BFXDEV-32 Fixed pfam missingcds. ID prefix + blast clusterCPU tag for guillimin and abacus
73ce180 Added chipSeq pipeline cleaning
9f6e203 Fixed rnammer missing modules hmmer 2.3.2 and trinity
jtrembla [email protected] 14 commits
6c0720b --arg for low abundant clusters. after 99% clustering. BFXDEV-31
d09db89 Added low abundance cluster cutoff argument. (After 99% ID clustering step). BFXDEV-31
9166850 Put more lenient parameters for itags QC to make it more 'universal' for most projects, especially those for which quality of reads 2 is low. BFXDEV-31
05e7b99 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
f60fa07 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
a996d3f Indentation correction. BFXDEV-31
38d8da8 Fixed parsing for blastdb command. BFXDEV-30
1b20686 Updated README for 454 data processing instructions. BFXDEV-31
8bafb19 Added even more description. BFXDEV-31
c003951 Added details to description of output. BFXDEV-31
fcd21e5 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
d9dcc9b Added step to filter number of blast results. BFXDEV-30
5d0c803 Removed --vanilla. BFXDEV-30
309ef5e replaced -num_target_seqs with -num_alignments. BFXDEV-30
Julien Tremblay [email protected] 1 commits
a16e5e9 Added --sampleSheet argument to getMiSeqBarcodes.pl BFXDEV-31
lefebvrf [email protected] 2 commits
b7f7d66 Changed TopHatBowtie.pm to put an end to the .fa.fa.fasta.fa symlinks madness when installing genomes. Parameter is now the bowtie index basename, consistent with the tool's documentation.
d29a172 Fixed dots in sample names bug BFXDEV-51
lletourn [email protected] 31 commits
3f785de Version bump to 1.4
38d0a8f BFXDEV-39 Fixed realigner when only one job is given
f728ac9 Updated bvatools
5e168e6 Tweak guillimin parameters
ea83ecd Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
1748e1a Updated parameters
69b8f2e Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
5da052a Adjusted cluster requirements
4cc7adf Removed useless param
4dace3e BFXDEV-256 Added step range to paired variants
cdbd4a0 BFXDEV-256 Added step range to paired variants
b535570 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
46d016c BFXDEV-254 Fixed GATK 3.2 change on CatVariants
10fb56b BFXDEV-252 Removed flagstat
125945f Fixed BAQ from pileup and ram from fixmate
71366af Changed picard to version 1.118 to fix the freeze when an exception occurs in asyncWriter
e9112eb BFXDEV-216 Removed per lane metrics
0568788 BFXDEV-245 Fixed uninitialized error when no bams are present
682a997 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
6d2b309 Fixed CCDS location
85578b8 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
54fde94 Merged master
407b9fe BFXDEV-236 optimized settings and split human builds
419e0a0 Added missing perl module
976ba1f Fixed missing HS metric, add 2 cores to bwa
9cf6dc5 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
c3fab1c Missing validation silent
5cfb61f Add genome versions of ini files
de4a383 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
dd39c54 Fixed typo in mergeAndCallGVCF section
3366970 Version bump to 1.4-beta
Marc Michaud [email protected] 1 commits
6b8f9f7 Add missing use
Mathieu Bourgey [email protected] 4 commits
3c0fb6e update ini to fit the new mugqic_tools tag 1.10.4 - BFXDEV-275
e5bd476 correct dnaseq bwa samnse dependency bug - BFXDEV-253
6fdf802 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
f3abd8c correct cuffdiff input double array issue when checking the job object is up to date
mathieu bourgey [email protected] 13 commits
3bd1f63 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
0e991b0 Update pairedVariant
469415f RNAseq replace headcrop at the good position in the trimmmomatic command; remove by default headcrop from the ini files - BFXDEV-267
534615d Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
402db54 PairedfVariant.pl: change where pindel get the insert size info - BFXDEV-266
87a9da6 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
192600e PairedVariant: allow mutec to run without cosmic file - BFXDEV-263
62e335d Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
9696dbc update dnaseq and paired variant ini files
37ad08b Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
21e3c79 remove conflicys in pipelines/dnaseq/pairedVariants.abacus.ini
a156ae5 pairedVariant.pl formAt SV and CNV to new standard - part of BFXDEV-41
cb5b91e cuffdiff now should not be relaunch in a restart if it exit correctly during the previous analysis BFXDEV-212
mmichaud [email protected] 14 commits
b9ef532 Fix genome path
ec31045 BFXDEV-269 Change genome files hierarchy
0234cd1 Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipeline
5eb75aa Fix usage to reflect new -s argument
f16ff09 Allow more ram for DepthOfCoverage
4033170 Fix CPU limit usage error by using less thread for the GC
88e5096 More RAM for QC (to avoid java heap space errors) + More threads and more walltime for mem (to avoid wall-time exceeded errors)
d946aa7 Run processing: Add option to force download of sample sheets
7feb923 Fix quote escaping in filter
8883201 Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipeline
0e60d3d BFXDEV-171 Trim index in the generated sample sheet according to the first/last index specified as parameter
c5a35cb BFXDEV-210 Use Parse::Range for steps to run, as all other pipelines
598ff88 Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipeline
8e8ca8e BFXDEV-211 Don't send email when jobs are successfully completed
[email protected] <pmarquis@abacus1.(none)> 4 commits
0cb571a Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
f934df3 MiSeq ini
1f34db5 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
31ae450 add ini MiSeq
[email protected] <pmarquis@abacus2.(none)> 1 commits
446b4d8 ppn=16 pour mem
Pascale Marquis [email protected] 1 commits
90e7a61 rm illuminaRunProcessingMiSeq_PM.ini
1.3 Mon Jun 2 10:02:07 2014 -0400 109 commits
Joël Fillon [email protected] 17 commits
9931258 Partial MUGQIC remote log for RRNATagger
da59f18 Remote MUGQIC Log Report in chipSeq, dnaSeq, pacBioAssembly, rnaSeq, rnaSeqDeNovoAssembly
521765d Updated RNA-Seq De Novo config files with latest module R/3.1.0
f59efb9 Updated rnaseq_denovo default config ini files with trinotate steps
0194584 More Trinotate steps in RNASeq De Novo
9a5cd2d RNASeq De Novo config files conflict solved + openjdk
1cfd288 Added file cleaning for RNA-Seq De Novo pipeline
4382d80 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
1092478 Solved conflicts when merging master
42e7aca Updated RNASeq De Novo pipeline with Trinity version 20140413p1
240d576 Beginning cleaning
e1c9021 Cleaning of cleaning...
ad6ed7a Fix on samToFastq/trimming dependencies in chipSeq pipeline
02d3cbe Added BAM file check in samToFastq
5e1aeb2 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into bam2fastq_basic
8ea8c98 Basic bamToFastq support for all pieplines
9afcd9e Version bump
jtrembla [email protected] 32 commits
6e3d8ed Added ini file for production purposes (QC assembly among others). BFXDEV-30
462ecaa fixed end step for BB. BFXDEV-31
06a4423 Added BigBrother modifs to RRNATagger pipelines. BFXDEV-31
e0c59ac Added sample counting in pipeline loop. BFXDEV-31
ebd465f Added a description of output files. BFXDEV-31
e0272b5 Fixes to itags_QC. decision if primers are present or not. BFXDEV-31
b199a3d mooooooore fixes. BFXDEV-31
d67905f more fixes to ini. BFXDEV-31
7b8a64c updated ini files. BFXDEV-31
609c204 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
befd271 Changed arg to adapt from percent to X hard cutoff.
16248cd Replaced percent cutoff by X cov cutoff. BFXDEV-30
d79cc38 added / updated ini files.
65ed0f3 ini files of RRNATagger changes. BFXDEV-31 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
9e30f84 updated ini files for RRNATagger. BFXDEV-31
37c1b0c Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
4cb24e1 ini file modif. BFXDEV-30
de66a9b update celera specs for hgap3. BFXDEV-30
0faaea6 Updated file check for restart at blasr ste. BFXDEV-30
83c0cbf Modified way seeds.m4.filtered is handled. BFXDEV-30
00482bd Updated ini file for pacbio assembly on guillimin. BFXDEV-30
9174116 fixed lib path. BFXDEV-30
f823b93 Fixed tab indentations. BFXDEV-30
5f8123d Upgrade pipeline from HGAP2 to HGAP3. BFXDEV-30
98d20c4 Removed unused SMRTpipe .xml files. Only keep filtering xml file. BFXDEV-30
468aacb Updated mugqic tools module.BFXDEV-30
a1ae253 Fixed output .mugqic.done file for pacbio dcmegablast. BFXDEV-30
e7426a8 Added module load perl in subroutines. BFXDEV-31
056cae4 added perl in ini files. BFXDEV-30
cf512b2 pacbio ini file for abacus. BFXDEV-31
85ebc8a Added blast parameters to ini files for guillimin. BFXDEV-31
52a9f7f Added blast step for pacbio rRNA tags data type. BFXDEV-31
Julien Tremblay [email protected] 6 commits
cc1fab0 updated ini file abacus.
9363d1f Updated ini file for abacus. BFXDEV-30
c3a1189 replaced compareSequences with pbalign for numthreads. BFXDEV-30
7189270 ini file for hgap3 on abacus. BFXDEV-30
37df4a8 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
1bf18fd Fixes to HGAP3. BFXDEV-30
lletourn [email protected] 38 commits
8f38558 Version bump to 1.3
c051f9a Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
42735dd BFXDEV-207 Fixed when interval lists are created
102ee1d Fixed gvcf bugs
613a990 Added emtpy quotes to empty keys so they don't become ARRAYs
b594056 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
d39b5d9 Updated BVATools version to 1.3
9eae448 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
9cc1832 BFXDEV-204 removed varfilter
82592ff Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
8b4f2bd BFXDEV-196 Added onTarget metric
2f57d4f Completed POD documentation
8176ab0 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
1d6793d BFXDEV-161 Added last steps to Haplotyper caller
240ca52 BFXDEV-198 Added simpleChrName in the ini since it was removed from the pm
7f0d539 Fixed params
39a7b38 BFXDEV-196 Added onTarget metric
8e7a04e Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
5825461 Ram was too close to max
db33ed9 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
89c5216 BFXDEV-193 Use new fixmate from bvatools. Fixed bad step dependency
ff9d44c BFXDEV-192 Added possibility to have extra flags in indel realigner
f30f24e BFXDEV-182 CollectMetrics sometimes needs to GC so 2 cores are needed
20768a4 Merged changes
de76e02 BFXDEV-181 Updated java vm version
d946871 BFXDEV-153 Added a way to ignore readset status
4ad3df1 BFXDEV-176 create MD5 on alignement
52b96be BFXDEV-174 Test that the data is valid
25f2a40 Merge branch 'master' into haplotypeCaller
d4a588d BFXDEV-168 added depth ratio plots BFXDEV-161 added haplotype caller
6596bf3 BFXDEV-166 fixed no index read, but one is associated
7b4bdc2 BFXDEV-162 fixed hiseq recognition
3ad3319 BFXDEV-157 Add callable region generation stats and BED in DNASeq
9f0e145 Added BVATools depth of coverage as a transition phase
17c7a8f Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
c775e18 Don't use BAQ since we use recalibration, this was decided awhile ago
1c6b7a4 BFXDEV-156 fixed csv encoding issues
46573b7 Updated settings for phase1 + phase2 merge of hardware
mathieu bourgey [email protected] 5 commits
35060f6 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
7faafe0 Create pipeline cleaning lib; partially implemented with RNA cleaning sub only BFXDEV-74
201124c Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
5177736 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
27c987a change how exit status is catched and exit the correct status in case of pipe discrepency BFXDEV-140
mmichaud [email protected] 11 commits
8c059d4 BFXDEV-155 Add rat and mouse alignment
4e9b1e1 BFXDEV-185 Separate config file (HiSeq, MiSeq)
637526f BFXDEV-164 Fetch sample sheets when they aren't specified and they aren't on disk
49e0b8c BFXDEV-183 Download each bed file only once
f87afda BFXDEV-184 Don't rsync Images folder. Was used on miSeq for debuging purpose
ae9782f BFXDEV-186 Don't use the BAM generated by markdup
c5d36af BFXDEV-180 Use processingSheetId as dependency id instead of sample name which isn't unique
6f3d923 Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipeline
ec78976 BFXDEV-171 Add option to specify first and last index
e3ad967 Add option to specify first and last index
d8eacb4 Run Processing: Add dependency on the metrics in the copy step, in case the markdup & BAM MD5 was already done in a previous pipeline, but not other metrics
1.2 Fri Mar 28 16:11:44 2014 -0400 200 commits
Francois Lefebvre [email protected] 2 commits
c18dfb6 RSEM more cpus on mammouth
9fff58f rnaseqdeno mammouth ini tweaks for trimming and RSEM
[email protected] <gleveque@abacus1.(none)> 3 commits
0072121 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
8bfdcff module load python in rnaseq.guillimin.ini --for htseq-count
bb66dcc rnaSeq.guillimin.ini changed default tmpDir --BFXDEV-144
Joël Fillon [email protected] 46 commits
2ca8f73 Version bump
0ce7d1a Solved conflict for merge master and bam2fastq branches
8696c9b Changed gzip to zip to compress rnaseq de novo outputs
d86c302 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
c09c292 Changed archive command from gzip to basic zip
63656f1 Minor fix: removed semicolumns in chipseq default config file
f383320 Removed unused variables and functions in all pipelines
3924dbe Added Version number in RNA-Seq De Novo Usage
3662f2e Minor mugqic/tools version update in rnaseq de novo ini files
9c9b747 Minor ini param adjustment + comment fix
be76b26 Removed hard-coded path to modules.sh: not required when invoked with Bash shell
56881db Updated default project paths with new /gs/ partition
4c24b2b Removed deprecated GetFastaAlias.pm
2d92ee8 Replaced shebang #!/usr/bin/perl with #!/usr/bin/env perl in all Perl scripts
6b7b376 Fixed bug SequenceDictionaryParser filepath with environment variables + set param [annotateDbNSFP] dbNSFP not mandatory
842ca5f Removed redundant file existence test in SequenceDictionaryParser.pm
851df47 Check all config modules only once when config hash is built, to reduce runtime
b5f3c9f Minor fix for adapters path in RNASeq De Novo config files
a86bd79 Updated adapters paths in RNASeq De Novo ,ini files
9d73b18 Added [Warning/Error] in msg display
d11cb76 Removed old lib/LoadModules.pm
1126cd9 More minor bug fixes for getParam validation
670c892 Fixed minor getParam validation bugs
e002a7a Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into valid_param
872d712 Added validation in all getParam functions
d9621c0 Fixed merge conflict in lib/Picard.pm
88411ce Added moduleLoad validation + major style reformatting
c130dc9 Added && between job commands to get right exit status
080410a Added param definition validation and module availability in LoadConfig
2ee8ea0 Added raw read dir and adapter file path validation in Trimmomatic lib
a461511 And more and more about parallel normalization
c32e316 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into sample_norm
8b316d0 Fixed metrics parent step
f6e131b Even more parallel normalization
da10fb1 More parallel normalization
5b5522c Normalization parallelized by sample
7ef8faa First draft of resume-jobs
39c49a5 Use module mugqic_dev/R until properly deployed
813d197 Fixed typo
3d51ae6 Fixed normalization stats file name
b667299 First stable RNA-Seq De Novo pipeline version
de50a89 Updated blast results and DGE matrices file names
04e1d5b Merged conflicted rnaSeqDeNovoAssembly.pl
d8717e4 Added POD documentation + fixed bug blast-longest-transcript file
cdc15b6 Added BLAST for longest transcript only, with results header
df03b3b Added metrics and deliverables steps in RNA-Seq De Novo pipeline
Johanna Sandoval [email protected] 1 commits
6a2eca8 README.md edited online with Bitbucket
johanna_sandoval [email protected] 5 commits
90ac5a4 BFXDEV-133 incompatibility between /usr/bin/perl and mugqic/perl/5.18.2. Added perl HOMER_HOME/bin/ to the program execution in peak annotations and motifs usign Homer
5e62ee0 BFXDEV-133 detected bug dependencies between trimming and alignment chipseq pipeline
972c98b Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
0fe7a1c BFXDEV-133 updated software, parameters, corrected bugs in chipseq pipeline for guillimin phase2
2401cf3 BFXDEV-133 adapt chipseq pipeline and configuration file to guillimin phase2
[email protected] [email protected] 17 commits
7f02064 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
ba4cfb0 bug in ini files: the following variables are not defined : genomeSize, annotation distances, markdup, report variables
942ef2a Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
050cc3c BFXDEV-123 add design example files to chipseq and rnaseq pipelines, update the user manual
599e532 BFXDEV-123 add design example files to chipseq and rnaseq pipelines
4006f00 BFXDEV-123 add design example files to chipseq and rnaseq pipelines
8290e24 BFXDEV-28 added PODS documentation to the dnaseq pipeline wrapper - typo
b79e9f7 BFXDEV-36 Generated PODs documentation for rnaSeq.pl wrapper
c1873ce BFXDEV-28 added PODS documentation to the dnaseq pipeline wrapper
5bfe14e changed my email by [email protected] in standard ini files
9d2232b BFXDEV-85 added flagstats/ generated a file with number of reads after filtering/mark as duplicates
1d069aa Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
6680dcf BFXDEV-84 correct bug for restart when merge lanes step failed
394b3ae BFX-1799 wrong variable initialization for genomeSize, detected when genome is not human or mouse
5ac34dc comment skip trimming step from standard ini files, added imagemagick to mammouth ini
e2b57e1 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
8c0e000 BFXDEV-77 bug in merge metrics, instructions to run Chipseq in the pipeline directory
jtrembla [email protected] 15 commits
8d91c82 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline Merge latest change prior to modifs to PyNAST (unset LD_LIB).
05f5335 Added unset LD_LIBRARY_PATH to PyNAST step. BFXDEV-31
8b79904 Updates to pacbio stats step. BFXDEV-30
956d5e3 Fixed pdf report for nc1. BFXDEV-31
c578e83 updated ini files for RRNATagger. BFXDEV-31
abb4b98 Added module load openmpi to PyNAST. BFXDEV-31
0eeea2e Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
cd179fc Added nozzle report for RRNATagger_diversity. BFXDEV-31
22b7fea Removed Iterator::Fastx from the wrapper as it is not even used here. BFXDEV-31
884627f fixed file checking for restart mechanism for sub loadPulses. BFXDEV-30
d275e03 fixed file to check for input in sub referenceUploader. BFXDEV-30
cab6153 Minor fixes to restart mechanisms. Removed inputFofn for filtering step and loadPulses step. BFXDEV-30
e9c1d81 Corrected some parameters for celera assembly step. now on lm2 by default. BFXDEV-31
752dd0a Implement module load and getParam checks. BFXDEV-31
8afc93f added missing path for abacus ini files. BFXDEV-31
Julien Tremblay [email protected] 33 commits
3cf8824 fixed path to primer files. BFXDEV-31
60e8f92 fwd and rev primers options now optional. BFXDEV-31
7f86972 Added modules for R and mugqic_tools to rarefactionPlots.R . BFXDEV-31
add6ebd mugqic.done fixes to rarefaction subroutines. Added mugqic tools module to appropriate subroutines. BFXDEV-31
72338c7 Updated help screen and removed appending ./scripts/ to PATH in curr dir. BFXDEV-31
6a982c8 Removed scripts/ dir and moved it to mugqic_tools
c99e920 minor fix for tmpdir definition. BFXDEV-31
8e3af42 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
f806248 minor fix to ini file (for mummer). BFXDEV-30
dabb656 Modifications to README and added mapping file example. BFXDEV-30
d3473a4 README for RRNATagger. BFXDEV-31
82ad834 Added RRNATagger (16S/18S/ITS rRNA amplicon) pipeline. BFXDEV-31
a9eeb68 fixes to ini files (pacbio pipeline). BFXDEV-30
a6bc0cc put only 1 mersize (14) in the gullimin ini files. BFXDEV-30
7bcfc65 Fixed bug with fofns. Minor modif to main loop. BFXDEV-30
126618d Changed /dev/null in the order of commands so no empty consensus.fasta anymore. BFXDEV-30
e9d2882 Forgot a && before gunzip in variantCaller step! . BFXDEV-30
907be7d Fix for uncompressed consensus.fasta.gz. BFXDEV-30
d5e5250 Fixes for compatibility with latest version of pacbio assembly pipeline. BFXDEV-30
fea30cc Fix for .bas.h5 files. BFXDEV-30
935aea0 Updates to PacBio assembly pipeline which now support multiple polishing rounds.
35d5972 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
28c7b82 Compute assembly stats from polished assembly and not unpolised ones. BFXDEV-30
ebdbae0 Fixed and updated pacbio ini file for abacus. BFXDEV-30
920b75f changed callVariants for variantCaller . BFXDEV-30
faf6c43 typo corr. BFXDEV-30
0b00031 Added additional instructions in the README. and changes relative lib path. BFXDEV-30
468184f Forgot to update this library for pacBio pipeline. BFXDEV-30
eda60c3 updated README. BFXDEV-30
6217fda corrected for typo gnuplot . BFXDEV-30
89f4c68 corrected relative path of lib folder
fdf9305 BFXDEV-30 modified parameters so they are more generic.
27ab913 Loop/dependency fixes to PacBio pipeline. Added compile stats step at the end of pipeline.
lefebvrf [email protected] 2 commits
5e46e90 necessary to honour cairo as X11 backend for R graphics with current module installation
8707d78 vanilla will hinder reading Rprofile.site, which in our modules will not be used to force cairo as X11 backend when available
lletourn [email protected] 27 commits
8c107ea BFXDEV-149 Fixed the way BVATools is called for coverage.
b839f5a Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
c7f0a75 Removed path test since they contain env variables
31322fb BFXDEV-124 fixed center when using mem
c2625cc Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
e420186 BFXDEV-116 Fixed reverse adapter
4f5f9d2 BFXDEV-111 Fixed many module versions
973c7b0 BFXDEV-114 Added R loading
4be23c3 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
419f6fe BFXDEV-109 Configured java version
b9989e5 Updated guillimin pipeline
7034346 Updated depth of coverage ini
db2b3a8 Fixed case when there are no BED files
b79a3a0 Fixed module typo
be34921 tmp hack so nanuq takes coverage graphs
8cf40e6 BFXDEV-89 BFXDEV-88 Change GATK to BVATools for DepthOfCoverage and support multi bed in project
7f45e96 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
b0a885e Added the missing mappability key
5b568ba Added line to keep overlapping pairs
73d736b Added umask to dnaSeq jobs
7e1f584 Updated module versions
67b9a78 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
472a3cd BFXDEV-73 Fixed undef jobId if step is up 2 date
a6e3c7c Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
2d9d66a Added details to the release guide
70f59da Version bump 1.2-beta
daabc8d Merge branch 'chipseq_report' of bitbucket.org:mugqic/mugqic_pipeline
mathieu bourgey [email protected] 14 commits
3cd0dee Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
22a87a0 DNAseq: correct SNVmetrics dependency BFXDEV-136; RNAseq: remove hstseq dummy/null module usage BFXDEV-137
cbdca41 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
3558370 DNASEQ: correct depthofCoverage missing bed file field in sample sheet BFXDEV-135
38db1aa ask bash to source /etc/profile.d/modules.sh BFXDEV-125
184fd53 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
3cbe61a add the -T option to cuffcompare BFXDEV-93 and validate previous commit for BFXDEV-47
a671e06 README.md edited online with Bitbucket
f9a7616 README.md edited online with Bitbucket
8f494a8 README.md add the bioinnfo email adress
6cb9d24 correct the 1st line typo in chipSeq.pl
f1df7ba Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
31f3438 replace ; by && in pipelines except for the rm of .done
8620232 replace a default ppn=20 by ppn=12 otherwise the job will never be launched
mmichaud [email protected] 33 commits
e242aa1 BFXDEV-147 Fix index mask of a single-index lane in a dual-index run
3c527b2 Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipeline
bce0666 Use new version of BVATools with simpleChrName support
0cf3980 RunProcessing: gentle perlcritic compliance
6e3b82e Fix BED file list from SampleSheet
4753244 Fix again the readsqc BVATools path
becd68c Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipeline
c8fc20f MD5 job doesn't need 5 cores, only one is ok
7b03a8f Fix readsqc using current session bvatools jar file instead of the one loaded on the compute node
230a617 Fix run processing when there is no target file
cb1be91 Merge branch 'master' into runProcessing
59829b2 Use new module loader for BVATools qc
61c25ba Add cranR module version
7e38002 Merge master into runProcessing branch
1261ab2 Support spaces in bed files
2b5b54e Don't align mice yet
9bb906f Support spaces in bed files. Fix bvatool module version
3e2571b Fix usage message (to show optional parameters) and print error message on dying
f549388 Die when there is a barcode collision. Fix bwa rgCenter for mem
172452b Add a parameter for the number of mismatches
da5e47a Default values for both sample sheets path
214c3d9 Merge branch 'master' into runProcessing
9584091 Update BWA module version
1a6989d Fix rsync command: quote character were not escaped correctly
a8e58fd Add missing depedencies for the copy job (metrics)
f19991c Don't create qc folder when the qc job will not run
7385c8e Depth of coverage: add reference parameter
7508bd4 Change '_' to '.' as seperators in the metrics job name
2ea6103 Enforce processingSheetId column in the sample sheet only when processing a run
f79fd8e BFXDEV-76 IlluminaRunProcessing Add target coverage metrics & change job ids to support multiple sample with the same name in the same lane
8e90e62 Merging upstream changes of the barcode metrics jobs. Less core and memory used, skip last read
5a2b132 Merging master into runProcessing branch
70383b3 BFXDEV-76 Illumina Run Processing Pipeline
Pascale Marquis [email protected] 2 commits
2172223 rnaSeq.guillimin_hg19.ini
d75c72d rnaSeq.guillimin_mm10.ini
1.1 Mon Dec 23 14:23:34 2013 -0500 137 commits
Joël Fillon [email protected] 69 commits
3051392 Commented code
78e706c Check rawReadDir value in configuration file
3e137a0 Minor R version fix
2eec3e9 Added trimMetrics step, fixed blast outfmt single quote bug
758a68b Added option file check, module availability check
7fabc9b Added genes/isoforms length values in edgeR results
faefc93 Added blast description in edgeR results
c54b336 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into rnaseq_denovo
e61eb0f Cleanup of rnaseq_denovo files
02ed5e6 Merge branch 'rnaseq_denovo' of bitbucket.org:mugqic/mugqic_pipeline into rnaseq_denovo
378d4d9 Updated ocnfig .ini files with trim parameters
2da3da4 Fixed missing escape $R_TOOLS
470df00 Fixed differential expression bug
36711d4 Added differentialExpression step
467076b Added multi-step dependency support
eba1405 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into rnaseq_denovo
003c41b Fixed Trinity.pm merge conflicts
6046b1b Added trim step + various fixes
efc7b74 Minor fix
5c140d0 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into rnaseq_denovo
e31fb3c Added guillimin config file + minor modifs
faf0d71 Updated .ini config files with cluster-dependant processing values
19f6b6d Merge branch 'rnaseq_denovo' of bitbucket.org:mugqic/mugqic_pipeline into rnaseq_denovo
dabafcf Added blastCPUperJob config tag
0eb0a4a Added blast step
01b495f Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into rnaseq_denovo
885d5f1 Updated default rnaseq tmpdir on guillimin: /sb/scratch/jfillon
7768316 Added first version of BLAST step
03e5423 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into rnaseq_denovo
0a05c4e Merge branch 'rnaseq_denovo' of bitbucket.org:mugqic/mugqic_pipeline into rnaseq_denovo
fcb3c5d Minor fix
dc1e136 Merge branch 'rnaseq_denovo' of bitbucket.org:mugqic/mugqic_pipeline into rnaseq_denovo
a80a6c2 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into rnaseq_denovo
29f179f Updated config ini files
63a2a5d Minor fix bowtie CPU
b3cf0fc Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into rnaseq_denovo
27fd66f Massive cleanup
f2eeb87 Another minor fix in mammouth ini file
60fac50 Minor fix mammouth ini file
2822aab Updated mammouth ini file
a7f4778 Added TrinityQC step + code reorganization
340a63d Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into rnaseq_denovo
9d7d75e Moved normalization parameters in config file
950b713 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into rnaseq_denovo
3fd9531 Fixed bug edgeR semicolumn
f850faf Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into rnaseq_denovo
c9e35cf Added edgeR step
42d400d Added rnaseq_denovo.mamouth.ini
a20391f Fixed bug unsorted list of fastq.gz from find
4a35ad6 Extended wall time for normalization and trinity
73bc9e6 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into rnaseq_denovo
db70b57 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into rnaseq_denovo
02f65b8 rsem prepare reference separately + job log relative path
ef38d5f First version of RNA-Seq de novo pipeline with normalization, trinity, rsem
39a95e7 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into rnaseq_denovo
74d4ac0 Further development of RNA-Seq de novo assembly
92aa251 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into rnaseq_denovo
e43a3e2 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into rnaseq_denovo
8946fc1 Further development of rnaseq_denovo pipeline
06fb9bc Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into rnaseq_denovo
d2a0332 Import of old deNovoAssembly in rnaseq_denovo branch
fc8082b Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into deNovoRnaseq
052b804 Minor fix
eddaed2 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into deNovoRnaseq
ab7f621 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into deNovoRnaseq
9eb1383 First draft of de novo RNA-Seq normalization
f4c998a Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into deNovoRnaseq
5873297 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into deNovoRnaseq
23f34b2 Fixed bug missing '\' before
Johanna Sandoval [email protected] 12 commits
29ff238 Readme for chipseq pipeline
6f007a9 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into chipseq_report
062d698 document mugqic pipelines setup using md - correcting bugs
30364fc Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into chipseq_report
fad747c document mugqic pipelines setup using md - correcting bugs
5a0a009 document mugqic pipelines setup using md - correcting bugs
f771f1a document mugqic pipelines setup using md - correcting bugs
848249a document mugqic pipelines setup using md - correcting bugs
58dca89 document mugqic pipelines setup using md - correcting bugs
9652290 document mugqic pipelines setup using md - correcting bugs
4cf001d document mugqic pipelines setup using md
4e9a82a Miscelaneous graphs chipseq pipeline
[email protected] [email protected] 21 commits
a5f8c70 corrected bug in qcTagsjobid
d3b16fd Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
ecd9434 Added PODs documentation to chipseq pipeline wrapper
3555ab4 correcting links to project's directories on README.md
1b94392 link to wiki on general README file
31db440 BFXDEV-63 Added -singleEnd flag when calling RNASEQC if parameter libraryType indicates single end reads
589689e added -singleEnd flag when calling RNASEQC if parameter libraryType indicates single end reads
eb5a068 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into chipseq_report
4e1e7df added variables for chipseq peaks annotation plots
ea839b3 corrected bug loading ReadMetrics and read metrics sample/run separator
9298aae Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into chipseq_report
0d69c52 commit chipseq report branch
95aab1a added annotation statistics + graphs to the chipseq pipeline
94bcb8b adapt chipseq pipeline to the new resume jobs functionality
73ee7a7 adapt chipseq pipeline to the new resume jobs functionality- config file
f1dabdd adapt chipseq pipeline to the new resume jobs functionality
4fe9953 Adapted chipseq pipeline to resume jobs changes
9d6f3d8 Transfer chipseq pipeline metrics libraries to the pipeline space
df472f0 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into chipseq_report
2e5f613 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into chipseq_report
67ae379 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into chipseq_report
Johanna Sandoval [email protected] 2 commits
2a5fbe0 document mugqic pipelines setup using md
6e68220 adding mammouth configuration file for chipseq pipeline
Julien Tremblay [email protected] 8 commits
1971ef1 Added memtime to dcmegablast and blastdbcmd. BFXDEV-30
9f0b66a Fixed unwanted mofifs to BLAST.pm. BFXDEV-30
b430c4c Modifications to perl packages for Pacbiopipeline. BFXDEV-30
bb5a19e Major modifications to the pacbio pipeline. Functional version tested on abacus and guillimin. BFXDEV-30
a17cd5a Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
97cd35a Added readme for pacbio assembly. BFXDEV-30
6432aad Remove my info fields in ini file. BFXDEV-30
67c11c1 Added PacBio assembly pipeline libs/wrapper/files, etc. BFXDEV-30
lletourn [email protected] 19 commits
4a6d8af Version bump 1.1
ef0d743 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
2541c18 BFXDEV-68 Added mutect to paired pipeline
d3998b6 Removed gpfs for guillimin
ed3de9b Fixed conflicts
11d0fe5 Fixed undef on steps that are up2date
bc77881 BFXDEV-67 use a true csv parser
bdbb7ce Merge branch 'chipseq_report' of bitbucket.org:mugqic/mugqic_pipeline
4d7c7fe Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
1a8cf59 BFXDEV-45 Fixed single read handling, fixed undefs
5d28000 BFXDEV-15 Changed the name of lane level bam metrics
ed46494 Fixed starting dependency and final job output
4555ab0 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
9252050 Added pre dependency and final sample output
aa452ff Changed BWA version for run processing and added some metrics
a29bac1 Added runprocessing parameters
ab65932 BFXDEV-52 DNAseq realignment restart generates duplicate unmapped bam
05272a8 BFXDEV-48 added missing close BFXDEV-49 added support for alignment+QC only RNASeqQC
e1ecac6 Version bump
mathieu bourgey [email protected] 6 commits
da9919d Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
fa47c13 replace ; by && - BFXDEV-47 and update the rnaseq ini files
e0ccc02 dnaSeq.pl correct typo (realign step) : BFXDEV-54
371c03f Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
799fca2 change/test replacing ; by && un command line
0a07178 Trimmomatic.pm remove single trimm bug
1.0 Fri Nov 8 15:03:24 2013 -0500 794 commits
David Morais [email protected] 2 commits
2620120 Merged in daveM_denovo (pull request #2)
0764a25 Merged in daveM_denovo (pull request #1)
David Morais [email protected] 94 commits
4c13dd1 remove entry
f458e98 added new entries
d8e671b split butterfly command lines in chunks
a963e53 creates BLAST best hits reports
61d9bf3 Fixed bug
5b9c160 Modify how the butterfly files are splitted
0234e16 fixed bug
5b2bbbc modify command line
f29fe2e fixed bug
f2bf4ab Added full path to groupInfo left and right samples
e8794a0 Added option for de Novo Assembly
3490e43 Implemented and tested Merge Trimming Remove duplicates de Novo assembly Blast BWA
8094aca fix paths
191bdcc fixed picard version and env variable
17934d1 change module add trinity
891bcf9 change module add blast
60bfa9f change module add blast
78f4ba6 change module add trinity
59905eb fixed typo
aacc3ec fixed typo
e78b5b6 Modified HtseqCount::matrixMake call. Now group is the last parameter so it can be left out.
c13eb91 Fix $group problem. Now if group is not specified the variable $group takes $sampleName value.
dcabd4b Fixed blast db error name
592659c perldoc
a94ec1d adding scripts needed by de Novo Assembly
a64a2ce add comments
289ec2f De novo Assembly config file sample. It needs to be modified according to your each project.
ba64039 mammouth_deNovoAssembly.ini
befb424 This is the main de novo RNA assembly pipeline. This is the first commit.
774254d modified config variable
5be92fd tidying up
7d190c5 tidying up
8d9704b tidying up
03fc63e tidying up
9b75e54 tidying up
24e31b0 tidying up
2cb0b70 tidying up
94a0d32 tidying up
6a8f8fc tidying up
24aa7af tidying up
42608a8 tidying up
2d3f8a9 tidying up
23e5b5e Coded full command line. Added sub contigStats
d0f849d Modified $laneDirectory
88bb2c7 Modified $laneDirectory
db5f506 Modified $laneDirectory in the singleCommand
bc774be Modified $laneDirectory to assembly/ and added $group variable to deal with groups on deNovoTranscriptome assembly.
55eb46d Modified perldoc
0ad8b58 Modified $laneDirectory
c21cab5 Modified $laneDirectory from alignment to assembly
2037ad6 Modified $laneDirectory
6bb3964 Modified $laneDirectory
229bba4 Assingned reads/ to $defaultDir
f0b1c61 Assigned $laneDirectory to 'reads/'
eb94920 Modified $laneDirectory = reads/
921adb0 new line
b187d45 Output bast results to /db directory
7c1754a change from own branch
c58b61f First commit. Library to create differencial expression analysis.
4086a94 Modified Doc
cc24e6b First Commit. Library to generate basic statistics on raw read count. Not Yet Ready for use.
1df2ca7 Library to create generate basic statistics of each sample. First commit. Not ready for use yet.
edf8193 Added the possibility of looping through more tha one DB. In This case the DB must be passed as an argument to the function.
3dac1f1 added comment
fccb0b1 removed quality offset from file name
db155a0 removed quality offset from file name
301427d added indexing function
e373c99 add function
34fd4a4 add function
986c00c add function
7183abe modify hash groupInfo
a77802b fixed input values
6bae877 BLAST lib, first commit
78008bd modify looping by group option
998b38a tiding up
6e243f5 fist commit Trinity
fb5182c change split setting
719e16b added new entries to sampleInfo hash
4bb98a4 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
644271f a simple multiformat file Spliter. First commit
8d3ccb3 Remove duplicate reads. First commit
cb8cfdf modify to work with nanuq sample sheet
56d16c8 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
80dd2fd First commit
7fbacf8 first attempt on STD
736365b Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
2c33bfc Reads the libraries form script_dir/lib
c3d669c added function that allows the script to read libs from the script dir
d9a378d add header
e32573a remove package folder
754f187 first commit. Lib to read module list
16372cb first Commit. lib to read config files
10e24cd change repo name
c56a0af adding space.
eric audemard <eaudemar@imac6-ub.(none)> 5 commits
f536084 add software install script : igvtools virusFinder SVDetect add genome install script : virus
2bd3239 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
f55f728 add install canFam3 and new bwa
7bdcac7 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
270bac9 adding deNovoSV pipeline from the mugqic_eaudem
Francois Lefebvre <flefebvr@abacus2.(none)> 4 commits
6f6477c febvre <ddcccccZZZZlefebvr@abacus2.(none)>
a4f6031 Integrated exploratory analysis step
1ea865b Changed Rscript -e template
a3468dc Fixed perl formatGtfCufflinks.pl call
Francois Lefebvre [email protected] 2 commits
d312e26 fixed problem when R packages list has duplicates
3fae3d0 Merged in module_install_scripts (pull request #3)
Francois Lefebvre [email protected] 53 commits
2ec42e9 duplicate section names
2a175b0 duplicate sampleOutputRoot
e9e50a1 duplciate param in ini
2abd12c duplicate sortSam sections in ini file removed
e8f8792 fixed bwa module name dnaseq.abacus.ini
5b3c1a9 kmergenie install script
810d081 updated rnaseq.abacus.ini wiggle chrsize path
8321d0f Updated R install script
d3087f7 R install script now installing Vennerable, gqSeqUtils, gqUtils from remotes.
9caf202 Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipeline into rnaseq_lef
b6591f3 Exploratory analysis step, still to test
ac2361f Added RSEM install script + updated Trinity one
789cb0f Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipeline into rnaseq_lef
6e37c42 no message
b014a95 Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipeline into rnaseq_lef
7d5e0aa Changed bwa to mugqic/bwa/0.7.5a, problem between RNA-seQC and 0.6.2
165e72d Updates R/Bioc script, now also installing all org packages
aa3dcc8 Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipeline into rnaseq_lef
2e48fa5 Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipeline into rnaseq_lef
92e196a no message
5d60cfa Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipeline into rnaseq_lef
8d4ef87 Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipeline into rnaseq_lef
5124369 Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipeline into rnaseq_lef
34000ad hg19 install script" add gtf mask for chrM, tRNA, rRNA for cufflinks
77f6acd Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipeline into rnaseq_lef
8165a03 Walltimes for htseq, cufflinks, cuffdiff too small for typical data
d99c877 htseq walltime
03aa1e1 Added 72h wall time align step
f70ac2f Updated bwa install script
5556091 Added blast module install script
a4cd056 Added few more R packages for install list
baaacb2 Removed MANPATH prepend from mugqic/R defnition
8eb8a25 chmod in in mugqic_tools.sh install script.
42d4ef9 <tools,perl-tools,R-tools,java-tools> from the svn now in tool_shed/
9b773f4 R packages lists updated
0725e01 Corrected bash_profiel for mammoth and changed R install script to 3.0.0
83cc87f Added R package "outliers" to R packages dependencies master list
5c1d4a6 Updated mammouth $MUGQIC_INSTALL_HOME value in guessing script.
bea7789 Few change to abacus wall time rnaseq
0e30bd7 Previous fix to Metrics.pm did not work
30f0bfb minor fix to Metrics.pm (will be depr. anyway at some point). chrome size file for wiggle left to default in default abacus .ini
16132ed Added -T sort unix sort in metrics.pm to correct problem on guillimin. Added job name suffixes in rnaseq.pl to make job names unique on Guillimin (dependencies)
60c84cc Merge remote-tracking branch 'origin/rnaseq_test'
ca2a4ac ..
59e116e Added hg19 installation
c83481d Added mm10 installation
c0dabe4 no message
c99255e updated to top hat 2.08 (bug in 2.07) + more genome scripts
57248b5 Added Eric's abyss install script
b20104a drafted genome installation script
e82f783 Corrected htseq module by adding module load python. Also started genome setup scripts
a4c4232 Finished python/numpy script. This script will not be 100% portable, need to set locate BLAS and LAPACK
6da084c Added modules/ directory to hold modules related content
Joel Fillon [email protected] 4 commits
c474058 Added java module in BWA lib + dos2unix rnaSeq.guillimin.ini
5bf363d Merge branch 'jobs_output' of bitbucket.org:mugqic/mugqic_pipeline into jobs_output
929fb10 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into jobs_output
5f3e86b Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into jobs_output
Joel Fillon <jfillon@abacus1.(none)> 4 commits
a051fa5 Added readRestartFile function
a7a1404 Print out MUGQIC command exit status.
f55bec0 Missing ";"
a7a2f6d Missing ";"
Joel Fillon <jfillon@abacus2.(none)> 1 commits
16641e8 Minor misspelling
Joël Fillon [email protected] 27 commits
67995c4 Added simple Perl script tool_shed/getLogTextReport.pl to create log reports
f7ddba6 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into logReport
3d61e71 Simplified getLogTextReport parameters
e12feca Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into logReport
aac70e2 Print out full job log path + 2 exit code outputs
d9e2d1a Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into logReport
75de931 Fixed lib/SubmitToCluster.pm conflicts
253bdfb Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into logReport
e7d552e Added number of jobs in log output
020e4e9 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into logReport
8ac8484 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into logReport
4991e38 Added timestamp in job log filenames .o
ae0b820 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into logReport
b42133b Reorganisation of job logs in an array
2db5f57 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into logReport
5d39c04 Added a few comments
bc9df34 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into logReport
f3998be Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into logReport
30cf022 Fixed exit status + walltime
39079a5 Added getLogTextReport function
3c10f40 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into logReport
964e92d Fixed package name
4c6b06b Merged master into logReport
5e38b43 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into logReport
70eff6e Added readRestartFile log function + Exit Status code in .o
d7f0f17 Fixed deliverable typo
5fd5004 added python tools path in mugqic_tools.sh
Joel Fillon [email protected] 8 commits
81a3ec9 Merge branch 'jobs_output' of bitbucket.org:mugqic/mugqic_pipeline into jobs_output
e19c7bd Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into jobs_output
2128dd2 Merge branch 'jobs_output' of bitbucket.org:mugqic/mugqic_pipeline into jobs_output
2235fc5 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into jobs_output
dab8f29 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into jobs_output
4cf3157 Check well-defined variables
7b03705 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
c4eaaeb dos2unix rnaSeq.guillimin.ini
Joël Fillon [email protected] 95 commits
a3fddd2 Removed Log lib (now merged in mugqic_tools/getLogReport.pl)
32f25ea A bit of a cleanup
8dbabd9 Synchronized rnaseq .ini files
c8fe2ba Fixed bug set @INC with relative path to mugqic pipeline lib
06ca9c5 Moved module and genome files to mugqic_resources repository
3f11508 Fixed bug missing '\' before
b163546 Standardization of rnaseq .ini file for the 3 clusters
6e7375f Removed prereq in module install script template
d76adbf Removed prereq + fix R module load to compile kmergenie
784d0c7 Updated Picard module install script now based on template
750caca Fixed inline comment bug in module install script template + fixed permissions in ea-utils module install script
6fc665c Fixed ea-utils compilation error on guillimin
24ab3fe Minor comment changes
dd1f730 Added ea-utils module install script + minor README change
a8533c2 Renamed MODULE_INSTALL_SCRIPT_TEMPLATE.sh + deleted old archive + minor fix
e6a1552 Added module file permissions
7e85ddc Created a module install script template; modified tabix install script
1b2f9bc Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
40b98e7 Deleted redundant modules/add_me_to_bashprofile.sh; added README.txt instead
e00d040 dos2unix all pipeline .ini files
1467393 Updated chipSeq pipeline .ini files with latest module versions
0133053 Updated rnaseq .ini files with latest module versions
ce59f4f Merged
e187b2d Minor change in R module install script
88ebc06 Changed permissions in R module install script
d5cfef1 Added vcftools module install script
8a5b369 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
a788a15 Added archive storage + permissions + cleanup in snpEff module install script
127d327 Removed unnecessary lib BiocInstaller for R install
f1bc1a0 Reorder chipseq modules in .ini files
ecb3c6b Removed duplicated modules in chipSeq .ini files
4280f36 Added archive storage + permissions + cleanup in Trinity module install script
1976a51 Added archive storage in UCSC module install script + update dnaseq ini file with bwa/0.6.2-ptx renaming
dfc61b0 Added archive storage in Trimmomatic module install script
64e9a66 Added archive storage in tophat module install script
04ba4a9 Added zip archive storage in picard module install script
d1c2d54 Added archive storage msg in GATK module install script
eed094d Added archive local storage in igvtools module install script
8bdeb5b Removed bedGraphToBigWig module install script (now part of ucsc module)
ff546a7 Added permissions in Tophat module install script
9c25d16 Updated dnaseq/validation.pl and dnaseq/pairedVariants.pl to comply with new version of SubmitToCluster
cbaf966 Added permissions in Picard module install script
7a726e6 Added permissions and cleanup in IGVTools module install script + minor changes
3709582 Added permissions and cleanup in hmmer module install script
34df850 Added permissions and cleanup in gemLibrary module install script + minor aesthetic changes
89ac0f9 Added permissions + minor fix in gatk module install script
ed0aeca Added permissions and cleanup in fastx module install script
d7dbb81 Added permissions and cleanup in fastqc module install script
bd89096 Added permissions and cleanup in exonerate module install script
ff61379 Fixed permission bug in UCSC module install script
568ef4e Fixed another permission bug in module install scripts
daa7cf2 Fixed bedtools install script bug for archives with different naming system
c3a3067 Added permissions and cleanup in cufflinks install script
1cb9cc5 Added permissions and cleanup in bwa install script
3ef584d Updated default pipeline .ini files with new mugqic/ucsc/20130924 for bedGraphToBigWig
942bc47 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
0eac0a1 Removed -j option in make; added kentUtils.Documentation.txt in bin/
e2253bc New install script for UCSC genome browser 'kent' bioinformatic utilities
7e1b165 Reorganized install scripts for a5, bedtools, blast, blat, bowtie, bowtie2
d097e82 Reorganized BEDtools install script
99f688c Removed last workdir parameter in chipSeq, rnaSeq; removed commented code; fixed blast+ bug in blast install module
a985b24 Added shebang in pipeline bash
27c480f Removed leading ':' in chipSeq JOB_IDS lists
669a97d Clarified bash by using job variables + header
6e72b67 Removed sampleOutputRoot tag in all .ini
ce93e25 Removed 'mkdir output_jobs' commented lines
89d60fd Merge branch 'jobs_output' of bitbucket.org:mugqic/mugqic_pipeline into jobs_output
68e948a Removed output_jobs subdirs in chipSeq pipeline + added job dependencies in log
c47fd5d Merge branch 'jobs_output' of bitbucket.org:mugqic/mugqic_pipeline into jobs_output
454e4ab Fancy install script from Johanna
e9f61b1 Merge branch 'jobs_output' of bitbucket.org:mugqic/mugqic_pipeline into jobs_output
054fbfb Removed final ';' in MACS2 cmd + aesthetic change
6e049a9 Merge branch 'jobs_output' of bitbucket.org:mugqic/mugqic_pipeline into jobs_output
8471e38 Removed ';' at the end of Homer cmds
ae79f34 Merge branch 'jobs_output' of bitbucket.org:mugqic/mugqic_pipeline into jobs_output
66a9193 Merge branch 'jobs_output' of bitbucket.org:mugqic/mugqic_pipeline into jobs_output
2445956 Merge branch 'jobs_output' of bitbucket.org:mugqic/mugqic_pipeline into jobs_output
310035f formatting changes + chipSeq redirect job output to specific location
830d57b ->
19f116e Minor formatting changes
890c915 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into jobs_output
995a8b4 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into jobs_output
a05a090 Added java module in BWA lib
622217d Reorganized job_output for DNAseq pipeline
405043d Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into jobs_output
8f6b4e5 Added tophat 2.0.9
6ef6c34 Minor formatting changes
e01c182 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline into jobs_output
9e220c5 Minor job parsing change
4af616a Added Job ID number in log
7ab1321 Redirect job list output into a specific file
7438d64 Job outputs go into jobs_output directory
967b888 Minor coding standardization changes
472a9b2 Minor error msg edit
abf1067 Moved getLogTextReport.pl in tool_shed/perl-tools/
Johanna Sandoval [email protected] 49 commits
8e63db4 changed config files to fit the new SubmitToCluster:initSubmit structure
98b7290 changed config files to fit the new SubmitToCluster:initSubmit structure
f2c2aa0 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
b56095e adapters small rna from Trimmomatic-0.22
61c25df Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
85c99b1 added module and installation script for gemLibrary
3998d3d Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
15e6a92 added chipseq.guillimin.ini parameters for hg19
152e3a7 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
7559eaf changed deseq.R : added flag comment.char=" " when reading edger_results.csv
b641ee2 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
e46c9c1 update install genomes script in tool_shed directory
9849932 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
f5bde35 prepend perl-tools directory to PERL5LIB
e819469 adapted ini file to changes in trimming parameters (headcrop)
af929ce Changed readstats module, added ReadMetrics.pm library
ef32d66 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
db61b39 Parsers or trimmomatic and flagstats reads statisttics, create a readstats.csv file
a8d8917 remove unused function (old tag directory generator)
dfc0b2e compute read stats using the ReadMetrics library
7faa225 prepend perl-tools to the PERL5LIB variable
b4c6417 corrected freeBayes install on guillimin
79ee5c6 Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipeline
e3e8549 Adapt install freebayes for Guillimin
f46883d Generate QC stats using R
3fa1222 Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipeline
09f7ec2 tag directory generation removed tmp sam file creation - added samtools
c3ca36b tag directory generation removed tmp sam file
d045ac1 Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipeline
8288285 Freebayes install and create module
237ed03 filter aligned unique reads using samtools
176e710 Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipeline
df89fcb added qc plots, corrected motif weblogo bug: seqlogo available on v 2.8.2
51077d3 generate chIPSeq QC metrics R script
6087d82 Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipeline
a99e139 Increase walltime for qctags generation
8e47a39 Initialize BWA_JOB_IDS per sample, create design 0 directories for MACS and annotations
143492d generate wiggle tracks: remove -i parameter
9666a94 Validate differences between design file and nanuq project file
c606dbd Validate missing values in design file
0f2715e adapt read statistics to changes in Metrics library
494d67e pbam flag for paired end reads on MACs
d0cfe12 chipseq pipeline configuration file for abacus
ed0bf0b chipseq pipeline wrapper
2665867 chipseq pipeline HOMER tags, annotations and motifs
dde6603 chipseq pipeline MACS2 peak calls
69e8682 uncommited changes, will control variable names from my scripts
aa273e9 Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipeline
70afa15 transform jobIdPrefix to avoid illegal bash variable names
Julien Tremblay <jtrembla@abacus2.(none)> 2 commits
fde3058 modifications to skip unnecessery bam merges.
cbdfb71 Added dnaclust install trace
lefebvrf [email protected] 3 commits
4edd2fd Fixed bowtietophat module, added cpu param to align, drafted template guillimin
136c03f test
d75425a Added Config-Simple and guillimin ini wc
lefebvrf [email protected] 5 commits
c7b8ab6 Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_pipeline into rnaseq_lef
63e674f quiet option is hard coded, makes it hard to diagnose cufflinks… -q could be enabled in previously added option parameter
bfc8e65 Cufflinks otherOoption parameter, to allow for instance for -M rRNA, MT, etc mask
62b1928 abacus htseq wall time increased from 3 to 12h
4ed3cba unused raw_count folder was created
lletourn [email protected] 174 commits
b07568d Added restart implementation
6633b73 Fixed pairedVariants with new structure
50e3e85 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
29fc49a Added release instructions
5833330 Removed deprecated code.\nAdded a version
6294737 Fixed step order bug
3a50453 Fixed region bug from previous commit
490b11e Added a way to skip trimming. Added a mem example
a385b07 Added a way to skip trimming
c60ac77 Merged master
a535288 Added lib barcode to lane data
441b96b Added missing ;
8fa3ded Updated old code
399a2d9 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
d9e7894 Fixed mem bugs
1c2a330 Fixed badly named CFG key
df22d10 Fixed paths for install. Crucial for these to work since they hardcode the paths
fbe736a Merged Master, some fixes and new dnaSeq report
9bcc238 Updated dbsnp
623de3e Amos install
0ffb61e Fixed region for torque
abd0940 Amos install
0370f0e Added split for stats
508f191 Fixed if test
2202926 Fixed dependant files
57f85c2 Fixed some bugs found while testing public datasets
e9d5b4e Fixed dir search order
dab8a76 Put appending and cleaning of dones in SubmitToCluster. More central, easier to maintain
2cd0d6b Fixed to support any year 2XXX
b9aafe9 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
1eb4c13 Merged master with outputDir fixes
ac70626 Merged HEAD, removal of job output dir
a4c2162 Change delimiter for regions, msub doesn't like colon
d1c131e Don't generate the pileup, it takes way too much space
9805b64 Added hg1k install and GNU parallel
2be9b17 Forced default picard buffer to the abacus optimal one
6230215 Finished updated the rnaSeq.pl pipeline
431b192 Merged master, added java module, dos2unix rnaSeq.ini
b2898cb Merged Master
cf0fca3 Finished implementing reset in dnaSeq
a2fc84a merged
fcd41d2 added missing calls for output dir
708959e added sampleOutput param to inis
ef0f696 Use the reight blat tools
5fdb7f3 installed v4 preview
8336865 Added beagle 3.3.2
ba10cb4 Refactored in the new Job object and input output file tests for restart
ea2786e Updated the way snp calling works to support, nb jobs instead of window.
f28a83a Removed dup index generation since we added recalibration
4a6c701 Fixed the way output directories are initialized
10f160f Updated version
0f80b86 Added pigz
b9e96e5 Merged master
9845505 Added PipelineUtil pacakge to all.\nCompleted BLASt implementation
d218799 Implemented per-job indel realigner Implemented multi sample snp calling Implemented per-job/per chromosome snp calling
3359fa3 Use ini for igvtools version Updated igvtools version for correct exit code
a3860f4 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
608ae55 Fixed already processed lanes.
66430db Version bump fixed execute bit
4ed8abc Trial implementation of new job restart flags
2e09503 Implemented restart job handling
9912c46 Added link to ptx patch
c984117 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
daa8f5a Added and updated modules
5448d09 Added tabix
35fa5c7 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
75c9afd Fixed many bugs
ae12147 Fixed many bugs
fb3af3a Fixed hash generation
42f88d8 Changed trimming
e7eb18f Fixed index vs ref problem
1dbc2b8 Fixed index vs ref problem
84c1895 Split metrics...we probably should split it further.
7747bcd Added TRINITY_HOME
70cd9b8 Added a parsable file containing trimming stats
d032c5a Fixed default params
9ea1211 Changed metrics position in steps
96ca681 Fixed parameter passing.
ea8cecc Fixed problems in RNASeq denovo pipeline
5cf8898 Added support for non-multiplex lanes....
1d8a190 Fixed trimmomatic bug Added usage to sampleSetup Fixed some ini params in rnaseq
a405492 Added options for skipping samples
4d7e1fa Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
d06a44f Fixed many issues and params for the RNASeq denovo
162142a Format stats from new format
7b61961 Version bump
972fa53 Added missing file warning
42b94f2 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
c347b1f Made many fixes to the denovo RNA Assembly pipeline
a995968 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
05042bf Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
7ec9500 Modified permissions
ceea8d2 Fixed mpileup bam location
58152cf Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
49b1409 Fixed parallele threads in single reads
e311d8d Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
d7e10f5 Fixed bwa mem RG bug.
8fa5378 Updated version
01e0dbd Added gatk to module list
8ff53e4 Fixed special single issue
1c6edb2 Added recalibration
36cbabd Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
f027679 Fixed generation for single ends
660ceda Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
8ef1373 Fixed validation for new project layout Added BWA mem support
89b8a33 Added snpEff and mutect Changed mode
070bcee Fixed output redirection
add31c7 Fixed multi runId resolution
351be7c Cleaned up downloaded genomes
40edd6e Sample setup scripts that works with miseq and hiseq and fetches the nanuq project by ID
69f8ad4 Added gallus gallus 3
a408a59 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
b3ee340 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
f461b67 Fixed default ref.
210079b Use parallele bwa by default
1d973c6 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
e83d068 Fixed libs and dna pipeline to use official project hierarchy
b0a33ed Fixed cleanup code
2af9a96 Updated the ray module
643a97b Added the exonerate module Fixed the ray module
5c1c619 Fixed append bug
41a888f Change file mode
12bdf75 Fixed configurable module load to trimmomatic Fixed pass output dir, not hard coded in trimmomatic
3f20c53 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
46ac74f Added missing rawReadsDir
6f4161d Partially fixed raw_read support for dnaSeq Fixed markdup call in dnaSeq
f861134 fixed conflicts
c973658 Fixed whole genome coverage
32b1e16 Added module versioning, fixed paired pileup bug
94c6f97 Added SV to the paired pipeline
2e99fd6 Added snv calling
2bfad55 Rolled back changes because it broke existing pipelines
0bc8182 Added SV to the paired pipeline
d67cedd Added DNAC support
79e909f Added DNAC support
b9b11aa Merge branch 'mugqic_lletourn'
0cceb49 Use job ids Added variant calling Added more flexibility when calling modules
18a60ab Added thresholds to genomeCoverage
a70bf88 Merge branch 'master' into mugqic_lletourn
275d08a Fixed usage
cee2b18 Added for snp calling
4e93043 Added metrics and steps to the dnaSeq pipeline
8222088 Change job dependencies from names to ids.
77a4c61 Fixed 2 paths bugs
30396f0 Don't use alternate contigs
0c43b15 Changed executable attribute
7b04c50 Keep dictionary ordering
f08a3ea Fixed usage message
4117265 Added paired snp variant calling
a5d2e16 Added more flexibility with tmp.
67b2b05 Completed first half of the validation pipeline Added adapters file for common paired adapters
d0df7f4 Added metrics to validation Added IGV tootls Added targetCoverage
d66f466 Fixed header
466071a Fixed issues with multi single+pair
df02765 Added Validation pipeline
b48e4b5 Merge branch 'master' of ssh://127.0.0.1:2222/mugqic/mugqic_pipeline
01ce3d4 Fixed index generation
0f46ad3 Merge branch 'master' of ssh://127.0.0.1:2222/mugqic/mugqic_pipeline
0067ebf Fixed timestamp checking
08d14e0 Added trim counts statistics
0923113 Fixed Trimmomatic MAJOR bug Added more settings to trimmomatic
275cd84 Use the right path for trimmomatic
f652072 Fixed output job directory naming
cc07363 Fixed bad realigner output file name
7c15b68 Merge branch 'master' of ssh://127.0.0.1:2222/mugqic/mugqic_pipeline
992ef66 Fixed bad argument
c4479ab Added guillimin conf file
5411b17 Fixed job dependency code.
53a75c0 Finished bam generation pipeline
faf8ed1 Merge branch 'master' of ssh://bitbucket.org/mugqic/mugqic_pipeline
4e30674 Added realigner
eda6d12 Fixed uninitialized bugs
2b17806 First pass for dnaSeq pipeline
5b1fc8b Fixed typo
Louis Letourneau <lletourn@abacus1.(none)> 1 commits
9286b83 Fixed many bugs
Mathieu Bourgey [email protected] 2 commits
3b2af18 RNASEQDN: modify trinity to check for previous assembly + variable name change
d49a53a TOOLS: chenge permission of non-executable scripts
Mathieu Bourgey [email protected] 26 commits
58770fe RNASEQ: change merge test
73407b0 RNASEQ: change merge test
54a772a Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
22f64a3 RNASEQ: add mkdir metrics in step 2
be482de Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
ee774f9 goseq.R: check and remove results that are not reported in the GO.db R package
220e9fb lib GqSeqUtils report call change
aa69e7e Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
08a72c9 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
20ce1c9 formatDenovoCombinedGTF.py update
3183fd0 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
f6ce3df RNAseq update
c833eee Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
d1e8dcc RNASEQ update unstrand wiggle bug correct
49d7bbc Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
e7dbfbc RNASEQ correct stranded wiggle array assignation
352f1ed add the java module call at Metrics::rnaseqQC
7825d84 add the java module call before at each picard function
aeb1c37 RNASEQ: add mamouth ini file
2f858ec MODULES - add temporary download folder in several module install scripts
e63d649 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
44263b2 rnaseq: resolve dependency pb
9873fc2 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
89fbe54 RNAseq modify some output location for the reporting
27bbc10 STATS: correct metrics:readstat for using output trimmomatic
772a5e5 RNASEQDN: old mamouth ini file by the new one that fit changes
mathieu Bourgey [email protected] 96 commits
ad59572 RNAseq update cuffdiff new dependency update
278c9d2 RNASEQ: change variable nemae of bowtie fasta
483e00d RNAseq update metrics stats
8b02e13 RNAseq update trimming metrics
2149362 RNAseq correct DESseq wrong dependency
398a121 RNAseq upstae trimming merge stats; update edgeR
b07481e rna update
bed41b6 rna update
4c45b56 remove tmp test for maty in dnaseq.pl
45c8ba2 rna update
ab2a149 R-tool: change saturation graph format
7d052f1 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
d0bd499 RNASEQ: add format protability to goseq
1cd3ae0 RNASEQ: add format protability to goseq
2c7b901 RNASEQ: add format protability to goseq
be3833a RNASEQ: add format protability to goseq
3289aac RNASEQ: add format protability to goseq
971938c RNASEQ: add format protability to goseq
6cc1155 RNASEQ: add format protability to goseq
9f84207 RNASEQ: rnaseq.pl update
e31e700 RNASEQ: rnaseq.pl update
fc1faad RNASEQ: add format protability to goseq
18ffd9a RNASEQ: add format protability to goseq
e725e01 RNASEQ: edger update
7fbbb5a RNASEQ: goseq update
c6dbccb Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
73a94bf RNASEQ: goseq update
06b2e4a RNASEQ: goseq update
f93dba0 RNASEQ: allow non native GOseq analysis
656c63c RNAseq: cuffdiff result fillter now include in the merge with fpkm
02e9ef8 RNAseq: cuffdiff result fillter now include in the merge with fpkm
bc787bd RNAseq update
49ab91f RNAseq update
e6515d3 change mugiqc_tools.install script to avoir facl conflict
9676b39 update tools changes
287a8e2 update tools changes
e35a443 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
58ad96b RNASEQ: resolve splited metrics dependency
4008a3d Rtools edger old index name not suported by the actual edger version now use
483781a RNAseq remove fpkm stats as they are done also in rna-seqc
c47230d RNAseq correct bugs - see BFXDEV-20 for details
8b614c0 RTOOL: mergeCuffdifRes bug correct && adapt the Rnaseq script in consequence 2
b5eee70 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
79804b1 RTOOL: mergeCuffdifRes bug correct && adapt the Rnaseq script in consequence
3b0ce98 RNASEQ: bowtie reference the new code should now be portable
4b6bf8e RNASEQ: allow readstat on single library
d079f59 RNASEQ: correct readstat output format
a61e005 RNASEQ: metrics changes bug correction & Cufflinks correction
28285f9 Metrics add argument
a1032f1 RNASEQ - correct typo in the mergebam step
68b309e Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
318f27b TOOLS remove type blatbestHit.awk
30a3793 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
5c8851c TOOLS adding blastbestHit.awk blatbestHit.awk
e8481fd Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
26152f7 RNASEQ: rnaSeq.abacus.ini correct rnaQC fasta variable name
9bcdcf9 TOOLS: gtf2tmpMatrix.awk - adapt for line witout gene name
57441b6 RNASEQ : adjust saturation plot title
f05e6a7 RNASEQ : add saturation thread Number in the abacus .ini file
1d072b2 Tools : make gtf2tmpMatrix.awk portable for various type of GTF file
fbf1e9a tools : adding gtf2geneSize.awk and gtf2tmpMatrix.awk which were initially in tools but not anymore in the module
2de9a90 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
3ec125d RNASEQ : allow running without reference GTF .2
a19c305 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
a48116d RNASEQ : allow running without reference GTF
4c9f803 pairedVariant - finish controlFREEC allow either bam or mpileup input everthing is specified in the ini file - BFXDEV-7
4a2439b R-tools change rpkmSaturation the count file need to be tab separeted
93eda90 R-tools correct the polting bug of the rpkmSaturation - BFXDEV-3
c67cdd0 rnaseq - replace my email by the MAIL variable
b1039a2 pairedVariant - add Control FREEC lib
75351f1 update rnaseq.pl for single mode
d155782 update rpkmSaturation to the last version
6714873 correct formatGTFCufflinks.pl
2220b26 Merge branch 'master' into mugqic_mathieu
8aef01e Merge branch 'mugqic_mathieu' of bitbucket.org:mugqic/mugqic_pipeline into mugqic_mathieu
7ff4088 correct rnaseq ; remove special caharacter in subimti to cluster job ID varable
39e7fd1 correct cuffdiff deNovo
9db7cdf correct conflict btw mugqic_mathieu and master
314eadc correct small bugs
0307f25 Merge branch 'mugqic_mathieu' of bitbucket.org:mugqic/mugqic_pipeline into mugqic_mathieu
17dadbe correcting pindel in lib/pindel.pm and in pairedVariant.pl form dnaseq pipeline
3927743 remove python module call in htseqCount::readCountPortable
ed644b5 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
fcc0e41 Merge branch 'master' into mugqic_mathieu
d7d4284 correcting last bug in rnaseq
4cb464e debug rnaSeq.pl
7725d78 trimmomatic add java module loading
1c9c334 submitToCluster add default value = if undef
70afb54 rnaSeq debug
2a78c37 resolve conflicts
3c840f2 Merge branch 'mugqic_mathieu' of bitbucket.org:mugqic/mugqic_pipeline into mugqic_mathieu
208d0cc debug
cc57bb2 update
8889bf1 rnaseq test debug; submitcluster modification; trimmomatic modifications
bd4afe1 debugging RNAseq
249ded6 debugging RNAseq
mathieu bourgey [email protected] 129 commits
a51199f samtools allow pileup with nb de region = 1 => pas de region
ea59d1f Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
3e902cc dnaseq.pl && samtools allow pileup with nb de region = 1 => pas de region
0ff4f48 upadte rnaseq.pl: missing convertion to new job object for stranded wiggle printToSubmit calls
ae5a4a8 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
f79aadb dnaseq annotation bug correct and ini update
d4e4586 rnaseq.pl: correct exploratoiy dependency if start at step 9
1b1abe4 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
33df28e dnaseq correct metrics restart bug & update dnaseq ini
6db6f70 remove tools_shed for the new tool repo
c653f58 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
e1bc285 metrics/SNVGraphs add input output test for restart
72b31c8 update Tools
0e1b10e Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
b758404 update cuffdiff stranded
af5dba2 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
371205c switch ToolShed to Tools
c0c1d65 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
665a098 RTOOLS update
3887f71 snvGraphMetrics.R update
38b94df DNAseq.pl update for metrics
4732109 DNAseq.pl update for metrics
daceb8a Merge branch 'dnaSeq_Report'
c82147a DNAseq.pl update for metrics and report
b31654c DNAseq.pl update for metrics and report
75f28e5 DNAseq.pl update for metrics and report
425b21e add tool_shed/python-tools/vcfStats.py
ac96abb remove mater to branch conflict
d133749 rnaSeq.pl edited online with Bitbucket
23e60fc remove conflict between danSeq_report and master
e67ddd8 add tool_shed/tools/splitSnpEffStat.awk
e4cfaee Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
f5ce57f GENOMES: add Tetrahymena_thermophila.sh
5f468e6 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
4bd157a sampleSetup.pl patch
a2dbacc samplesetup correction
f4ba095 Trimmomatic.pm edited online with Bitbucket
00d0af0 merging matser in dnaseq_report
7ff833e rnaSeq.pl edited online with Bitbucket
4556bda DNArepport update
91d8b3c goseq.R edited online with Bitbucket
e2148e7 goseq.R edited online with Bitbucket
5a202eb DNAreport update
a7a6d13 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
cc7af8d TOOLs gtf2geneSize.awk protability
05fdcce RNAseq update
8b603f9 RNAseq update
58cc9c6 RNAseq update
dcf225d Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
b69a50b RNAseq correct htseqcount for stranded RNA
f452010 RNAseq Strand-specificity correction
7754be2 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
bc5c5a5 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
a5450ec TOOLS rpkmSautrationadd more flexibilty on the file format
4960f3e RNASEQ: add output directory creation in fpkm folder
904595f General : Get back the change lost in commit 0007ea2
84818ac Revert "RNASEQ: correct dependency issue"
d45c5d7 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
d3b3bb1 Revert "RNASEQ: correct dependency issue"
7aabc00 save before revert
0007ea2 RNASEQ: correct dependency issue
a3c5a79 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
eb6d023 RNASEQ : add deliverable + test exploratory
f62067d Merged in rnaseq_lef (pull request #4)
63a0163 RNASEQ - GqSeqUtils.pm update
23099ae RNASEQ modify exploratory for the pull request #4
80da056 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
af49cae RNAseq update
c258e2c REDO lost commit: rnaSeq.pl use absolute path of design file
7e28edd SubmitToCluster.pm edited online with Bitbucket
79e8b60 add log.pm lib
19289aa add logfile for cluster output file path
ccf1fa8 RNASEQ: rnaseq.pl update
5e8fcfc Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
2896458 RNASEQ: make design file path an absolute path to conflict if the working directory does match the relative path of the file given in argument
363892b rnaSeq.pl edited online with Bitbucket
6435ebe RNASEQ: rnaseq.pl && cufflinks.pm update
3e54a64 SubmitToCluster.pm edited online with Bitbucket
9ac95ff RNASEQ: rawCountMetrics update
509b645 RNASEQ: rawCountMetrics update
c484eed Merge branch 'logReport' of bitbucket.org:mugqic/mugqic_pipeline into logReport
6e725ad Merge branch 'master' into logReport
a7faedc RNASEQ: mv dgeMetrics (step 10) as rawCountMetrics (step 8)
04752e2 add log.pm lib
3fcc283 add logfile for cluster output file path
c527ebc RNAseq: change wingzip call in the metrics
cbbd97a RNAseq update rnaseq.pl
f4e3215 RNAseq: update rnaseq.pl
2a8c65c RNAseq: update rnaseq.pl change matrixreadcount form step 10 to 7
b43088a RNAseq update rnaseq.pl
f672d80 RNAseq: update rnaseq.pl
5535e50 TOOLS: add formatDenovoCombinedGTF.py & RNAseq: update cuffcompare
a348a62 RNAseq: update rnaseq add cuffcompare
cb485b8 rnaSeq.pl edited online with Bitbucket
177aa34 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
0c0f4a1 TOOL: Adding thepython tools folder and the getRefBinedGC.py script in it
77b49e2 Merge branch 'mugqic_mathieu'
1ebe60b Merge branch 'mugqic_mathieu' of bitbucket.org:mugqic/mugqic_pipeline into mugqic_mathieu
22ad9e5 update RNA
36d735d RNASEQ: add correct cpu request for alignment
e171861 correcting sv code small bugs
553a3b0 finish breakdancer filter and add pindel to dnaSeq
ce1cd91 start adding breakdancer filter and pindel to dnaSeq
59fa224 resolve Htseqconfilct
0ad6350 merge with mugqic_mathieu
c1a278a debug the code
1498b14 Merge branch 'master' into mugqic_mathieu
c2b1cc4 resolve lib/SubmitToCluster.pm conflict
4df938a resolve HtseqCount conflict
3268ff4 try to update local master to real master
97b4432 everyhting except delivrable are done; debugging
a0a5544 goseq done; 1st test on going
eb5785e metrics: done; General module nomeclature conversion
5efae81 metrics: updates; SAMtools: add viewFilter sub function ; tophatBowtie: bug correction and simplification
2e48636 metrics updates
be331d2 matrix done; DGE done
4223cc7 fpkm done; DTE done ; DGE on going ; metrics on going
08778dc correcting wiggle; fpkm and rawCount done ; DTE on going
1ed2d7f wiggle done
cd318c1 update metrics ini.file and few correction tophat/botwite
052889d merging ok ; metrics started; new functions and changes in the picard lib
2f6709a merging done ; metrics started
66ea6a4 update to the master branch
7166f74 Tophat-botwie done; merging started
f9662b8 uppdating TopHat lib and rnaSeq.abacus.ini
634a238 uppdating my branch
9f81ed0 Starting bowtie/tophat lib
43c3e7a Global dependency and RNAseq Triming and submit with working directory argument
d6a6324 starting the rnaseq pipeline
Mathieu Bourgey <mbourgey@abacus2.(none)> 1 commits
f36f0e2 rnaseq.pl debug; Metrics debug; Picard debug; SaMtools debug; SubmitToCluster debug; TophatBowtie debug
Maxime Caron <mcaron@abacus1.(none)> 2 commits
4ad23e1 test
0b8c7fb test
Pascale Marquis <pmarquis@abacus2.(none)> 5 commits
168ea11 Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
221a12e Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
b91d4da Merge branch 'master' of bitbucket.org:mugqic/mugqic_pipeline
0b27236 zorro.sh
9f170dc Tetrahymena_thermophila.sh