32 tags, 316 commits
HEAD Sat Apr 22 14:48:35 2017 -0400 0 commits
2.1.8 Mon Apr 24 09:55:28 2017 -0400 18 commits
Edouard Henrion [email protected] 1 commits
edfb29a commiting the CHANGELOG before release
Mathieu Bourgey [email protected] 10 commits
9ec9b5f correct ggplot
e638845 correct ggplot
eafb4fc correct typo
7f025be correct typo
1b9f6b8 correct typo
9f98c73 correct typo
dd2ba39 correct typo
170f2b4 correct typo
5e77a35 correct typo
9ccb828 correct module incompatibility
mathieu bourgey [email protected] 7 commits
70af3b5 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
69cce81 update gene titan
068bd1b Imporve Genetitan processing script
4c049c5 Imporve Genetitan processing script
446f05d resolve conflict merging
94240fc Updat Axiom tools for more QC
3f461c4 add somatic signature R tools
2.1.7 Fri Jan 20 16:31:19 2017 -0500 19 commits
Edouard Henrion [email protected] 10 commits
2689de8 MUGQIC_TOOLS - added fixVS2VCF.py to python-tools as it is needed in the tumor_pair pipeline
eae6a16 commit prior to mugqic_tools 2.1.7 release
aa281e5 deseq.R - added '-l => local fit' parameter explanation to the tool manual
79f0a77 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
91e39ac DESeq.R - using 'locfit' to allow locat fit instead of just having to use parametric dispersion
0db2adb Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
1791395 DESeq & Edger - explicitely importing 'methods' library because Rscript does not
5f65c6e Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
0e76111 metaMArkerSeq - correct shebang for heatmap Rscript creation
7f27678 ampliconSeq - krona debug
mathieu bourgey [email protected] 6 commits
6f9a78d Add R script to filter Gene Titan processed data
a21249f Add bash script to process gene titan
1e3420b Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
ff2f40d R-tools - remove typos in RunSequenza_analysis.R
18d5720 make runBlast to support no empty fastq 3rd line
822983a adding sequenza analysis script
[email protected] [email protected] 1 commits
efc56e0 Adding vcf2bed.pl script for varscan2 of tumor_pair pipeline
Tushar Dubey [email protected] 2 commits
026180c removed subset line from script PopSV
8e0170c Added PopSV script(beta)
2.1.6 Tue May 3 14:55:43 2016 -0400 11 commits
Edouard Henrion [email protected] 7 commits
a929638 new CHANGE LOG prior to new release 2.1.6
39ac81a resolve conflicts
362d40a commiting changes prior to new release
1c82601 new CHANGELOG.md
354ce82 corrected a bug in chipSeqgenerateAnnotationGraphs.R that caused a blank exon annotation graph - BFXDEV-501
b0c47cc mugqic_tools - up-to-date CHANGELOG.md
ab85318 ading a changelog to mugqic_tools (since v2.1.5)
Mathieu Bourgey [email protected] 1 commits
df62d30 dict2bed - correct bug and add feature - BFXDEV-521
mathieu bourgey [email protected] 3 commits
96eadd0 R-tools - update SNV metrics to the new stats output fromat from snpEff - BFXDEV-490
99b25f3 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
e45cf73 Rtools - remove typo and allow to skip insert size when working on single end library - BFXDEV-502
2.1.5 Thu Jan 21 14:47:39 2016 -0500 2 commits
mathieu bourgey [email protected] 2 commits
b7a6767 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
6863562 perltools - remove # character from blast hit results - BFXDEV-500
2.1.4 Fri Jan 8 12:28:52 2016 -0500 2 commits
Edouard Henrion [email protected] 1 commits
7d49d89 adding of ampliconseq tool
[email protected] [email protected] 1 commits
4c1e35d added script to generate gemini compatible vcfs
2.1.3 Wed Nov 25 16:43:54 2015 -0500 3 commits
mathieu bourgey [email protected] 3 commits
12e7e61 Removed SNVstats error with missing lat line in the list file - BFXDEV-120
c0f12ba Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
653c15d Adding python-tools/mergePairedSingleTrimFastq.py a tools to interlace paired fastqs and also concatenate single fastq in one majopr fastq after the trimming
2.1.2 Tue Sep 22 11:32:36 2015 -0400 16 commits
Francois Lefebvre [email protected] 1 commits
84ff003 pacBioAssemblyStats.pl edited online with Bitbucket
Francois Lefebvre [email protected] 1 commits
f2710d9 Fixed bug where annotations could not contain # char
Johanna Sandoval [email protected] 11 commits
bbdd52b BFXDEV-397 filtered tab separated assembly file extension must be tsv not xls
bb8b1ee BFXDEV-397 join filtered isoforms and isoform counts matrix to generate exploratory analysis on filtered transcripts
2ce156d BFXDEV-397 filter components using trinotate annotations generate a fasta and tab separated filtered assembly file
2042d52 BFXDEV-397 extract sequences from assembly using python SeqIO, generate tabular and fasta filtered assembly
a6d8d13 BFXDEV-397 added functionnality to filter files using python expressions, applied to parse Trinotate Output and to parse and merge csv files
6b44025 BFXDEV-396 filter trinotate output to create a file with IDs of annotated transcripts given a set of rules in the ini file, added to parseMergeCsv the functionnality to rename columns that have the same name in input files (R make.names like)
444b013 BFXDEV-396 parse merge csv, corrected errors in sort by when join gets None
65337cf BFXDEV-396 parse trinotate output, read isoforms length and print only the longest isoform per gene in annotations, added a standard parse plus merge csv files python program
08d2c29 PRJBFX-1075 mugqic_pipeline tests, scripts used to setup automatically a test directory (sync data and programs)
4b82c77 BFXDEV-396 parse trinotate output to obtain gene annotations, transcript annotations and goterms
65055cb corrected issue in validateBAMContent.pl when any field in the sample sheet contains a comma BFXDEV-406
lletourn [email protected] 2 commits
187363f BFXDEV-367 added year directory flexibility
52d8592 BFXDEV-370 Added a way to generate split bed files from a dictionary file
ptranvan [email protected] 1 commits
c6d9982 BFXDEV-434 Script for amplicon-seq pipeline.
2.1.1 Wed Mar 25 12:14:14 2015 -0400 3 commits
Francois Lefebvre [email protected] 1 commits
64b89fa changed threshold test to allow reporting FDR of 1
lletourn [email protected] 1 commits
5d67c83 Fixed bug, array was interpreted instead of using @ as a character
mathieu bourgey [email protected] 1 commits
fd4b011 python - rRNacounter.py - correct issues when missing transcript Id or Name in the gtf and add a shorten version of the stat file <OUTPUT>_short.tsv
2.1.0 Mon Mar 9 15:58:31 2015 -0400 5 commits
Joël Fillon [email protected] 2 commits
b8cd478 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
556d49d BFXDEV-59 DNAsampleMetrics.R fix
Mathieu Bourgey [email protected] 1 commits
1fe0c67 python - update rrnaBAMcounter.py to include all unmapped reads in the total count
mathieu bourgey [email protected] 2 commits
95a1618 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
721a2b3 python - add rrnaBAMcounter.py a small tools to report rrna counts
2.0.3 Fri Jan 30 10:55:17 2015 -0500 9 commits
Joël Fillon [email protected] 1 commits
3bce44e BFXDEV-292 Updated MACS2 file paths in R-tools/chipSeqgenerateAnnotationGraphs.R
lletourn [email protected] 4 commits
79092c7 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
8896743 Added output file name instead of redirection to allow stream buffering
5266243 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
70fd054 File needs to exist in paired file to add columns
Mathieu Bourgey [email protected] 1 commits
b38b144 TOOLS - update tools/gtf2tmpMatrix.awk to support commetn lines in the gtf
mathieu bourgey [email protected] 3 commits
b11c11c Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
6d02639 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
b115892 Tools -add runLumpy.sh using v0.2.9 of Lumpy and the python script for the mean and stdev
2.0.2 Tue Dec 16 16:43:51 2014 -0500 7 commits
Joël Fillon [email protected] 2 commits
3d45241 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
133314b Fixed line names of PacBio read count statistics in pacBioAssemblyStats.pl
lletourn [email protected] 5 commits
bee0f73 Merged
ec283d9 Added check for remaining bams
b353c17 changed shebang
394e526 Removed smtps code
1c25d6a Added name test
2.0.1 Wed Dec 10 13:55:58 2014 -0500 1 commits
Joël Fillon [email protected] 1 commits
3d37484 Fixed bug rpkmSaturation.R read.table with options quote='', comment.char=''
2.0.0 Fri Dec 5 16:50:16 2014 -0500 5 commits
Joël Fillon [email protected] 2 commits
e72d9d7 README.md edited online with Bitbucket
c559d56 Moved getLogReport.pl nanuq2mugqic_pipeline.py into mugqic_pipelines/utils/
lletourn [email protected] 1 commits
2798ba3 BFXDEV-285 Added BED download to nanuq2mugqic
mathieu bourgey [email protected] 2 commits
e18c5e4 R-tools - goseq.R : remove conflict
ac10aed R-tools - goseq.R : allows more flexibity in fdr and p-value for goseq AND remove native goseq approach - BFXDEV-289
1.10.5 Wed Nov 19 17:45:08 2014 -0500 5 commits
Joël Fillon [email protected] 3 commits
df16cb8 Fixed read.table parsing with more options in goseq.R
3cc7d88 Renamed readset and design file 'SampleID' column into 'Sample'
66a0ef5 Minor cosmetic change in nanuq2mugqic_pipeline.py
lletourn [email protected] 2 commits
0fe9969 fixed multi region sample problem.
7f9d6f1 fixed multi region sample problem.
1.10.4 Mon Oct 27 10:14:56 2014 -0400 8 commits
Joël Fillon [email protected] 4 commits
4bd19a3 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
4c856bb Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
2895b24 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
69045a5 Change column name Sample -> SampleID
lletourn [email protected] 3 commits
5b7edf2 Removed dependency
248b569 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
0cabf7b Added configurable depth
Mathieu Bourgey [email protected] 1 commits
6a5a015 gtf2tmpMatrix.awk: add a space to underscore replacement - BFXDEV-275
1.10.3 Fri Sep 19 14:26:49 2014 -0400 2 commits
mathieu bourgey [email protected] 2 commits
f9e7384 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
3549781 R-tools/DNAsampleMetrics.R: allow dots in sample names - BFXDEV-265
1.10.2 Thu Sep 18 14:20:04 2014 -0400 21 commits
eric audemard <eaudemar@imac6-ub.(none)> 2 commits
5b255ea Merge branch 'master' of https://bitbucket.org/mugqic/mugqic_tools
8142961 fixe bug for puure
Joël Fillon [email protected] 5 commits
b41f22a Fixed some wrong shebangs with #!/usr/bin/env ... + moved fasta_Length_select.py in python-tools/
ff00af7 Added Pacbio support in python-tools/nanuq2mugqic_pipeline.py
e20a00c Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
0b7d384 Minor nanuq path update
79ea08e Added project ID in filenames created by nanuq2mugqic_pipeline.py
lletourn [email protected] 14 commits
ef5b466 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
b2df75a BFXDEV-257 fixed 'track' bed header handling
102d25f Fixed sampleName source from validateBAMContent.pl
9dcdfeb Added sampleSetup filters
228da50 Fixed STARTTLS
878bcac Fixed bad line
9a9d8f3 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
12514d2 Add smtp server setting to tool
91925ce Fixed relative path bug
dabdf6a Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
f5f2705 Added a tool to track BAM contents vs a sampleSheet
e286095 Added a usage computation script
f072cf0 BFXDEV-239 fetch bed files automatically
d2f5483 Fixed bug
1.9.3 Wed Aug 13 15:40:58 2014 -0400 0 commits
1.10.1 Wed Aug 13 15:42:47 2014 -0400 23 commits
eric audemard <eaudemar@imac6-ub.(none)> 3 commits
50a26f2 add awk script for puure pipeline
aec0ad3 rm tempory file
f086553 add python and R script for PUURe
Francois Lefebvre [email protected] 1 commits
e47fc25 check.names=FALSE in rpkmSaturation.R to avoid sample names renaming
Joël Fillon [email protected] 5 commits
10b2015 Minor help formatting in nanuq2mugqic_pipeline.py
e04b1d1 Renamed nanuq2readset.py into nanuq2mugqic_pipeline.py
0651d43 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools into python
a3c469b Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools into python
4e195ec Added nanuq2readset.py
jtrembla [email protected] 6 commits
75b61db Added bam to fastq script.
149c76d Added argument for low abundance cluster cutoff after 99% clustering step. BFXDEV-31
0db65b3 Fixed bug when selecting Fungi in OTU tables for 18S analyses. BFXDEV-31
91a3cb0 Minor fix for cluster counts in report table. BFXDEV-31
a3977a6 Added 454 option to sampleSetup.pl. BFXDEV-31
49576a9 Added script to keep best n blast hit from blast tables. BFXDEV-30
Julien Tremblay [email protected] 4 commits
5f77252 fixed verbose level. BFXDEV-31
bef496e Added --sampleSheet argument to getMiSeqBarcodes.pl . BFXDEV-31
5ecef7e Improved script to merge 454 fastqs prior to do 16S/ITS analysis. BFXDEV-31
705ebbe Refined support for 454 libs. Works with amplicon data at least... BFXDEV-31
lefebvrf [email protected] 1 commits
aae7d76 Added naive interface script to gqSeqUtils::calculateGenelengthsFromGtf
mathieu bourgey [email protected] 3 commits
03494cb perl-tools/csvDepthFilter.pl
c2acd2c README.md edited online with Bitbucket
9dea6af README.md edited online with Bitbucket
1.10 Thu Jun 5 15:20:49 2014 -0400 7 commits
jtrembla [email protected] 1 commits
7c2b7cc BlastCov.tsv is now sorted. BFXDEV-30
Mathieu Bourgey [email protected] 2 commits
bb3351c Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
5855f97 Add tools/WG2ChromosomeFasta.awk to split wholeGenome fatsa into chromosme fasta
mathieu bourgey [email protected] 3 commits
f583128 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
66cf8b6 DNAsampleMetrics.R will add NA filed if missing file of CCDS metrics - BFXDEV-214
7fc08bd R-tools/deseq.R and R-tools/edger.R now support numeric sample name starting with 0 in the design file - BFXDEV-213
[email protected] <pmarquis@abacus2.(none)> 1 commits
f18b168 genome length R script
1.9 Thu May 22 15:52:21 2014 -0400 32 commits
Joël Fillon [email protected] 2 commits
8dedf91 Reformatted FASTQ/BAM check in sampleSetup.pl
36496aa sampleSetup with BAM/FASTQ support
Johanna Sandoval [email protected] 1 commits
90ca70d Automatic install genomes assumes that variable MUGQIC_INSTALL_HOME is already set, commented the prologue section
[email protected] [email protected] 2 commits
0bbfb7a Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
e761d84 BFXDEV-133 Bug detected in guillimin phase2 : LoadConfig must not be used outside pipeline wrappers
jtrembla [email protected] 17 commits
2e10fea Fixed indentations RRNATagger scripts. BFXDEV-31
96a2cc3 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
8c234b8 Modified percent cutoff to X cov. BFXDEV-30
72beb43 Script to add sample names to a vcf file. Have to provide a sample list in a separate txt file.
0c40368 Fixed XML file output. BFXDEV-30
6427884 Added option to output the runId. BFXDEV-30
05c9794 Added estimated coverage in one of the generated tables. BFXDEV-30
e1b188b Added script to add coverage in blast table (pacbio pipeline). BFXDEV-30
ca16e2b Addition of script to merge FPKMs from an RNASeq project.
d1544d0 Wrote script to merge many raw count matrix (form the RNASeq pipeline). PRJBFX-699
ad33ba8 Script to compile Ray results.
73e465d R script to plot histogram of contig length (use with ray output).
bda1da9 Minor fixes. BFXDEV-31
67647b1 Cut pacbio reads to 2000 nt max. Because of crash in downstream qscore fastx step. BFXDEV-31
83520b1 Added verbosity for debugging. BFXDEV-31
623fa15 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
fdefc43 added script template to perl tools.
Julien Tremblay [email protected] 2 commits
9d508fb Added script to preprocess pacbio reads to make them compatible with RRNATagger pipeline. BFXDEV-31
ea38231 Modified pacBio samplesetup so it can output ccs reads as well. BFXDEV-31
lletourn [email protected] 8 commits
f5bbfb7 BFXDEV-196 Added onTarget calculations
2228327 Deprecated
4d5c477 Added tool to add basefreq to vcf2csv generated file
09a3ce7 Added CAF support
86af2d2 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
7a25aa5 Fixed sample data validation
609e706 Added paired version of vcf2csv
ce20505 Added check on columns for FASTQs and BAM files
1.8 Fri Mar 21 10:50:47 2014 -0400 24 commits
Joël Fillon [email protected] 6 commits
60d4c2b Fixed minor mug in mergeTrimmomaticStat.R: don't raise error if metrics directory already exists
272534a Fixed exit code parsing with string instead of digits, in case of negative value
9deeadd Fixed exit code parsing on guillimin phase2 + added job status
a7232fe Replaced shebang #!/usr/bin/perl with #!/usr/bin/env perl in all Perl scripts
38e99ca Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
596ae25 Added bam support in sampleSetup.pl
johanna_sandoval [email protected] 2 commits
f82a5ac Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
90e9ade corrected bugs found installing genomes on Guillimin
[email protected] [email protected] 2 commits
c847345 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
65393b6 Convert vcf generated by the standard pipeline (samtools+snpeff+snpsift annotations) to a tab separated file
jtrembla [email protected] 5 commits
a3ffbfc Modified summary table in pacBioAssemblyStats.pl. BFXDEV-30
6250902 Updates to pacbio scripts. BFXDEV-31.
69d9699 Fixed font size. BFXDEV-31
77f3a7e Added OTUheatmap.R for RRNATagger pipeline. BFXDEV-31
5ffccd1 added plotTree.R for RRNATAgger pipeline. BFXDEV-31
Julien Tremblay [email protected] 2 commits
f6f56c0 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
1938c7b tool to plot coverage bed files. BFXDEV-30
Mathieu Bourgey [email protected] 3 commits
64d2d44 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
4edc18e R-tools/DNAsamplemetrics.R: change the alignment and duplicates metrics which where not good when mem is used correct BFXDEV-130
8f31f92 remove unneccessary file integrity in vcfstats.py
mathieu bourgey [email protected] 4 commits
fe831ce Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
90c9d92 chipSeqgenerateAnnotationGraphs.R : add additional control for empty file with size > 0
3c5d163 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
6f4cab2 add null buffer in vcfstat.py; correct BFXDEV-120
1.7 Thu Feb 27 14:21:48 2014 -0500 22 commits
Joël Fillon [email protected] 1 commits
11a876c Added count of successful/active/inactive/failed jobs in getLogReport.pl
[email protected] [email protected] 6 commits
adf0ba6 BFXDEV-118 corrected typo : Error in ccdswgbase500[nameLoc] = statsValue[[1]][12] : object 'ccdswgbase500' not found
4ffbc51 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
8979f4a BFXDEV-82
1e5bb9a BFXDEV-90 additional parameters could be added when downloading fasta sources. Use exonerate to create the byChr fasta files
869df6b set and unset IFS to add extra parameters for wget
6d2e5f2 add the byChr directory using the exonerate's fastaexplode tool
Julien Tremblay [email protected] 8 commits
060424c Added sampling of 5000 reads instead of 1000 to determine if phred 64 or 33. BFXDEV-31
ac0e6f6 Added tools associated for RRNATagger pipeline. BFXDEV-31
1d195ad Script showing which perl modules are currently installed (based on your PERL5LIB env.).
6103763 Tool to fetch MiSeq barcodes having the runId in hand. Generates barcodes fasta file for that run. BFXDEV-31
0b13647 Added debug info in STDERR so we can "more easily" associate Xpercent values with X cov. values. BFXDEV-30
d21120c Fixes for contigs N25, N50, etc. Support for multiple polishing rounds in stats ouput. BFXDEV-30
a41ff66 Modified path in which script looks for basx files (i.e. /2014/..) BFXDEV-30
877029f Updated scripts to compute stats from polished assembly. + added HGAP cutoff value in X (cov). BFXDEV-30
mathieu bourgey [email protected] 7 commits
7137697 add a checking step for a correct add of the change rate file name at the end of vcfStats.py. because sometime it doesn't works and don't give exit code 1 - BFXDEV-120
355ef9d Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
bcbc074 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
18dbf68 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
9dfc311 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
630ede6 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
b1da309 update R-tools/deseq.R round count to allow RSEM estimates
1.6 Thu Jan 16 11:50:26 2014 -0500 20 commits
Joël Fillon [email protected] 4 commits
81edd0d Added option to keep unsuccessful jobs only
31c1a92 Use array instead of hash for memtime values
b0b7273 Added --success option + updated memtime lines with MEMTIME prefix
1c1ca04 Added in log report lowest/highest memory jobs, queue, limits and many other columns
[email protected] [email protected] 1 commits
9b03a64 bug: bwa and bowtiw indexes in their respective directories
Julien Tremblay [email protected] 7 commits
6301360 updated pacbio R script to generate plots. BFXDEV-30
f8f88f5 Added one missing \t in header line when --memtime option. BFXDEV-30
5284a79 Removed STDERR debug lines . BFXDEV-30
fdf618d Creates symlinks in raw_reads now.
1c99b73 Added support for memtime output in job output files. BFXDEV-30
0b47d59 Added script that extracts and compile assembly stats from multiple assembly done with the pacbio assembly pipline.
d3561c8 Updates to pacbio scripts for pacbiopipeline. BFXDEV-30
lletourn [email protected] 2 commits
40eb4ad BFXDEV-81 Force encoding of Text::CSV
d6175d8 BFXDEV-60 added error handling in blast script
mathieu bourgey [email protected] 6 commits
20bee87 remove integer formating edger
be18ef7 remove iunteger formating deseq
46cdbfe rounding and formating raw_count-matrix object to allow RSEM output
92150f5 edger.R edited online with Bitbucket
83a3709 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
2cff02b update R-tools/deseq.R R-tools/edger.R tools/gtf2geneSize.awk
1.5 Wed Dec 4 17:31:54 2013 -0500 9 commits
Francois Lefebvre [email protected] 1 commits
fae748f removed method='deviance' and robust=TRUE. Dispersion estimates otherwise crashed with large number of tested features.
Joël Fillon [email protected] 2 commits
36107a7 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
97dd764 Added missing executable permissions on some scripts
Julien Tremblay [email protected] 6 commits
b3c7b21 Remove die if missing xml files. BFXDEV-30
3734d18 Fixed some display aspect of plots. BFXDEV-30
5d38409 Plot data on filtered reads only. BFXDEV-30
e2c59ba Now accepting bax.h5 files. BFXDEV-30
21e25c1 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
9afd05f Added coverageFraction options. BFXDEV-30
1.4 Tue Nov 26 16:15:09 2013 -0500 14 commits
Joël Fillon [email protected] 4 commits
32bd762 Added parallelBlast.pl from David Morais
8aa30c7 Added extra virtual memory percentage
1f5c951 Minor fix
e75b39c Improved text log report with human readable durations and memory size + ratios
Julien Tremblay [email protected] 10 commits
baa2e84 Added parsing feature for xml file. BFXDEV-30
124242b Removed print debug lines.. BFXDEV-30
30df1a6 Added fastq support for hgap cutoff. BFXDEV-30
d205d97 Fix because new columns where added on nanuq samplesheets. BFXDEV-30
e55569b Fixes + compute reads stats directly form .tsv. BFXDEV-30
1cc0b4b Skip $filteredSummaryTable if file does not exists. BFXDEV-30
bcfd86d minor fix. BFXDEV-30
f30195f Minor fix to plot script. BFXDEV-30
af895cd Fixes to PacBio scripts. BFXDEV-30
3154bf0 Skipped header line for DNAsampleMetrics.R. Plus a bunch of fixes for pacBio perl scrips...
1.3 Tue Nov 19 11:26:09 2013 -0500 11 commits
Joël Fillon [email protected] 1 commits
ba0c093 getLogReport now handle job output relative paths
[email protected] [email protected] 5 commits
8d1ab10 chipseq annotations plots : changed graphs title-font size
ab07c78 Print header on read/alignment metrics
16ce33c chipseq annotations plots : changed graphs title
d628bb6 Plots of annotation stats chipseq pipeline
72db555 added parser for chipseq annotations - narrow peaks
Julien Tremblay [email protected] 2 commits
e5924a1 Added sequence iterators.
86b53d8 Added R script to generate pacbio reads distribution plots. More to come...
lletourn [email protected] 1 commits
83fa74f Added a more verbose explanation of sampleSetup
mathieu bourgey [email protected] 2 commits
83f5bed Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
885d006 correct vcfStat.py exception - BFXDEV-50
1.2 Mon Nov 4 16:03:51 2013 -0500 11 commits
Joël Fillon [email protected] 2 commits
59ae2f0 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
4ba58a2 Moved former Log lib into getLogReport.pl
[email protected] <jtrembla@abacus2.(none)> 1 commits
e92437f Added EOL ($) for each patterns to not consider .mugqic.done files.
lletourn [email protected] 2 commits
853f9ad Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
fb1406b Added library barcode support
mathieu bourgey [email protected] 6 commits
4a29ecd Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
5bda081 update edger.R
6a456ff R-tools/snvGraphMetrics.R update
0ee0703 remove the double $ patern in DNAsampole Metrics
ef7d3e1 Merge branch 'master' of bitbucket.org:mugqic/mugqic_tools
445a476 snvGraphicMetrics.R add robustness to single sample analysis
1.1 Thu Oct 24 14:02:21 2013 -0400 1 commits
mathieu bourgey [email protected] 1 commits
c87cd72 correct typo in DNA Metrics script
1.0 Thu Oct 24 10:50:35 2013 -0400 1 commits
mathieu bourgey [email protected] 1 commits
52f686f add regex to avoid .done captation and rename the tag from v1.0 to 1.
v1.0 Tue Oct 22 16:20:47 2013 -0400 3 commits
mathieu bourgey [email protected] 3 commits
1902529 Rtools snvGraphMatreics.R for the dnaSeq pipeline
7dfaa57 update snvGraphs
bde9560 update SNV metrics