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__version_info__ = (1, 3, 7) | ||
__version__ = '.'.join(map(str, __version_info__)) |
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#!/bin/bash | ||
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PERL5LIB=$PERL5LIB:/path/to/SOAPfuse/1.27/source/bin/perl_module; export PERL5LIB | ||
PYTHONPATH=/path/to/Anaconda/2/2018/lib/python2.7/site-packages/ | ||
export LD_LIBRARY_PATH=/path/to/Atlas/lib:$LD_LIBRARY_PATH | ||
export PATH=$PATH:/path/to/ncbi-blast/2.8.1+/bin/ | ||
export R_LIBS=/path/to/R/R-3.5.1/lib64/R/library | ||
export R_LIBS_USER=/path/to/R/R-3.5.1/lib64/R/library | ||
# Here you can add all commands which should be executed for each individual slurm job | ||
# e.g. module load R/3.6.0 | ||
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module purge | ||
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module load anaconda/2/2018 | ||
module load bioinf/star/2.6.1d | ||
module load bioinf/samtools/1.9 | ||
module load R/3.5.1 | ||
module load java/11.0.1 | ||
PYTHONPATH=/path/to/your/python/packages/ | ||
export PATH=$PATH:/path/to/be/added/ |
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# 4) To whom shall slurm mails be sent to (receiver) | ||
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[general] | ||
version = 1.3.6 | ||
pipeline_name = EasyFuse | ||
tools = QC,Readfilter,Fusioncatcher,Star,Starfusion,Infusion,Mapsplice,Soapfuse,Fetchdata,Summary | ||
fusiontools = Fusioncatcher,Starfusion,Infusion,Mapsplice,Soapfuse | ||
fd_tools = Fusiongrep,Contextseq,Starindex,ReadFilter2,ReadFilter2b,StaralignBest,BamindexBest,RequantifyBest | ||
tools = qc,readfilter,fusioncatcher,star,starfusion,infusion,mapsplice,soapfuse,fetchdata,summary | ||
fusiontools = fusioncatcher,starfusion,infusion,mapsplice,soapfuse | ||
fd_tools = fusiongrep,contextseq,starindex,readFilter2,readFilter2b,staralignBest,bamindexBest,requantifyBest | ||
sender = [email protected] | ||
receiver = [email protected] | ||
min_read_len_perc = 0.75 | ||
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# execution command for individual programs (what you write here should be identical to what is typed in the console) | ||
[commands] | ||
# for python | ||
python2 = /code/miniconda3/envs/py27/bin/python | ||
python3 = /code/miniconda3/bin/python | ||
# for qc | ||
fastqc = fastqc | ||
skewer = /code/skewer-0.2.2/skewer | ||
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@@ -85,4 +87,4 @@ fusioncatcher = /ref/fusioncatcher_index/ | |
[other_files] | ||
infusion_cfg = /ref/infusion.cfg | ||
soapfuse_cfg = /ref/soapfuse.cfg | ||
easyfuse_model = /code/easyfuse/data/model/Fusion_modeling_FFPE_train_v33.random_forest.model_full_data.EF_full.rds | ||
easyfuse_model = /code/easyfuse/data/model/Fusion_modeling_FFPE_train_v35.random_forest.model_full_data.EF_full.rds |
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name: conda_env | ||
channels: | ||
- anaconda | ||
- bioconda | ||
- conda-forge | ||
- defaults | ||
dependencies: | ||
- _libgcc_mutex=0.1=conda_forge | ||
- _openmp_mutex=4.5=2_gnu | ||
- argcomplete=2.0.0=pyhd8ed1ab_0 | ||
- argh=0.26.2=pyh9f0ad1d_1002 | ||
- bbmap=39.00=h5c4e2a8_0 | ||
- bcftools=1.9=h68d8f2e_9 | ||
- biopython=1.73=py37h14c3975_0 | ||
- blast=2.13.0=hf3cf87c_0 | ||
- bowtie=1.2.3=py37h9a982cc_2 | ||
- bowtie2=2.3.4.3=py37he860b03_1 | ||
- bx-python=0.8.2=py37hebb334c_2 | ||
- bzip2=1.0.8=h7f98852_4 | ||
- c-ares=1.18.1=h7f98852_0 | ||
- ca-certificates=2022.9.24=ha878542_0 | ||
- curl=7.85.0=h7bff187_0 | ||
- entrez-direct=16.2=he881be0_1 | ||
- expat=2.4.9=h27087fc_0 | ||
- fastqc=0.11.9=hdfd78af_1 | ||
- font-ttf-dejavu-sans-mono=2.37=hab24e00_0 | ||
- fontconfig=2.14.0=hc2a2eb6_1 | ||
- freetype=2.12.1=hca18f0e_0 | ||
- gettext=0.19.8.1=h27087fc_1009 | ||
- gffutils=0.10.1=pyh864c0ab_1 | ||
- gmap=2021.08.25=pl5321h67092d7_2 | ||
- gsl=2.5=h294904e_1 | ||
- htslib=1.9=h4da6232_3 | ||
- importlib-metadata=4.11.4=py37h89c1867_0 | ||
- importlib_metadata=4.11.4=hd8ed1ab_0 | ||
- keyutils=1.6.1=h166bdaf_0 | ||
- krb5=1.19.3=h3790be6_0 | ||
- ld_impl_linux-64=2.36.1=hea4e1c9_2 | ||
- libblas=3.9.0=16_linux64_openblas | ||
- libcblas=3.9.0=16_linux64_openblas | ||
- libcurl=7.85.0=h7bff187_0 | ||
- libdb=6.2.32=h9c3ff4c_0 | ||
- libdeflate=1.13=h166bdaf_0 | ||
- libedit=3.1.20191231=h46ee950_2 | ||
- libev=4.33=h516909a_1 | ||
- libffi=3.2.1=he1b5a44_1007 | ||
- libgcc-ng=12.1.0=h8d9b700_16 | ||
- libgfortran-ng=12.1.0=h69a702a_16 | ||
- libgfortran5=12.1.0=hdcd56e2_16 | ||
- libgomp=12.1.0=h8d9b700_16 | ||
- libidn2=2.3.3=h166bdaf_0 | ||
- liblapack=3.9.0=16_linux64_openblas | ||
- libnghttp2=1.47.0=hdcd2b5c_1 | ||
- libnsl=2.0.0=h7f98852_0 | ||
- libopenblas=0.3.21=pthreads_h78a6416_3 | ||
- libpng=1.6.38=h753d276_0 | ||
- libsqlite=3.39.4=h753d276_0 | ||
- libssh2=1.10.0=haa6b8db_3 | ||
- libstdcxx-ng=12.1.0=ha89aaad_16 | ||
- libunistring=0.9.10=h7f98852_0 | ||
- libuuid=2.32.1=h7f98852_1000 | ||
- libzlib=1.2.12=h166bdaf_4 | ||
- lzo=2.10=h516909a_1000 | ||
- mapsplice=2.2.1=py37h07887db_0 | ||
- ncurses=6.1=hf484d3e_1002 | ||
- numpy=1.21.6=py37h976b520_0 | ||
- openjdk=11.0.1=h516909a_1016 | ||
- openssl=1.1.1q=h166bdaf_0 | ||
- packaging=21.3=pyhd8ed1ab_0 | ||
- pandas=0.24.0=py37hf484d3e_0 | ||
- pbzip2=1.1.13=0 | ||
- pcre=8.45=h9c3ff4c_0 | ||
- perl=5.32.1=2_h7f98852_perl5 | ||
- perl-apache-test=1.43=pl5321hdfd78af_0 | ||
- perl-app-cpanminus=1.7046=pl5321hd8ed1ab_0 | ||
- perl-archive-tar=2.40=pl5321hdfd78af_0 | ||
- perl-base=2.23=pl5321hdfd78af_2 | ||
- perl-business-isbn=3.007=pl5321hdfd78af_0 | ||
- perl-business-isbn-data=20210112.006=pl5321hdfd78af_0 | ||
- perl-carp=1.50=pl5321hd8ed1ab_0 | ||
- perl-class-load=0.25=pl5321hdfd78af_1 | ||
- perl-class-load-xs=0.10=pl5321h9f5acd7_6 | ||
- perl-class-method-modifiers=2.13=pl5321hdfd78af_0 | ||
- perl-common-sense=3.75=pl5321hdfd78af_0 | ||
- perl-compress-raw-bzip2=2.201=pl5321h87f3376_1 | ||
- perl-compress-raw-zlib=2.202=pl5321h166bdaf_0 | ||
- perl-constant=1.33=pl5321hdfd78af_2 | ||
- perl-data-dumper=2.183=pl5321hec16e2b_1 | ||
- perl-data-optlist=0.112=pl5321hdfd78af_0 | ||
- perl-db-file=1.855=pl5321h779adbc_1 | ||
- perl-devel-globaldestruction=0.14=pl5321hdfd78af_1 | ||
- perl-devel-overloadinfo=0.007=pl5321hdfd78af_0 | ||
- perl-devel-stacktrace=2.04=pl5321hdfd78af_1 | ||
- perl-dist-checkconflicts=0.11=pl5321hdfd78af_3 | ||
- perl-encode=3.19=pl5321hec16e2b_1 | ||
- perl-eval-closure=0.14=pl5321h9f5acd7_6 | ||
- perl-exporter=5.74=pl5321hd8ed1ab_0 | ||
- perl-exporter-tiny=1.002002=pl5321hdfd78af_0 | ||
- perl-extutils-makemaker=7.64=pl5321hd8ed1ab_0 | ||
- perl-file-path=2.18=pl5321hd8ed1ab_0 | ||
- perl-file-temp=0.2304=pl5321hd8ed1ab_0 | ||
- perl-getopt-long=2.52=pl5321hdfd78af_0 | ||
- perl-io-compress=2.201=pl5321h87f3376_0 | ||
- perl-io-gzip=0.20=pl5321h7132678_4 | ||
- perl-io-zlib=1.11=pl5321hdfd78af_0 | ||
- perl-json=4.09=pl5321hdfd78af_0 | ||
- perl-json-xs=2.34=pl5321h9f5acd7_5 | ||
- perl-list-moreutils=0.430=pl5321hdfd78af_0 | ||
- perl-list-moreutils-xs=0.430=pl5321hec16e2b_1 | ||
- perl-mime-base64=3.16=pl5321hec16e2b_2 | ||
- perl-module-implementation=0.09=pl5321hdfd78af_3 | ||
- perl-module-runtime=0.016=pl5321hdfd78af_2 | ||
- perl-module-runtime-conflicts=0.003=pl5321hdfd78af_1 | ||
- perl-moo=2.005004=pl5321hdfd78af_0 | ||
- perl-moose=2.2201=pl5321hec16e2b_2 | ||
- perl-mro-compat=0.15=pl5321hdfd78af_0 | ||
- perl-package-deprecationmanager=0.17=pl5321hdfd78af_1 | ||
- perl-package-stash=0.40=pl5321h87f3376_1 | ||
- perl-package-stash-xs=0.29=pl5321h87f3376_1 | ||
- perl-parallel-forkmanager=2.02=pl5321hdfd78af_1 | ||
- perl-params-util=1.102=pl5321h9f5acd7_1 | ||
- perl-parent=0.238=pl5321hd8ed1ab_0 | ||
- perl-pathtools=3.75=pl5321hec16e2b_3 | ||
- perl-role-tiny=2.002004=pl5321hdfd78af_0 | ||
- perl-scalar-list-utils=1.63=pl5321h166bdaf_0 | ||
- perl-set-intervaltree=0.12=pl5321h87f3376_2 | ||
- perl-storable=3.15=pl5321hec16e2b_3 | ||
- perl-sub-exporter=0.988=pl5321hdfd78af_0 | ||
- perl-sub-exporter-progressive=0.001013=pl5321hdfd78af_1 | ||
- perl-sub-identify=0.14=pl5321hec16e2b_2 | ||
- perl-sub-install=0.928=pl5321hdfd78af_3 | ||
- perl-sub-name=0.21=pl5321hec16e2b_3 | ||
- perl-sub-quote=2.006006=pl5321hdfd78af_0 | ||
- perl-try-tiny=0.31=pl5321hdfd78af_1 | ||
- perl-types-serialiser=1.01=pl5321hdfd78af_0 | ||
- perl-uri=5.12=pl5321hdfd78af_0 | ||
- perl-xsloader=0.24=pl5321hd8ed1ab_0 | ||
- pip=22.2.2=pyhd8ed1ab_0 | ||
- pyfaidx=0.7.1=pyh5e36f6f_0 | ||
- pyparsing=3.0.9=pyhd8ed1ab_0 | ||
- pysam=0.15.2=py37h633085e_10 | ||
- python=3.7.8=h6f2ec95_1_cpython | ||
- python-dateutil=2.8.2=pyhd3eb1b0_0 | ||
- python-lzo=1.12=py37he0a3664_1004 | ||
- python-xxhash=1.4.3=py37h8f50634_1 | ||
- python_abi=3.7=2_cp37m | ||
- pytz=2022.4=pyhd8ed1ab_0 | ||
- pyvcf3=1.0.3=pyhdfd78af_0 | ||
- readline=8.0=h46ee950_1 | ||
- samtools=1.9=h10a08f8_12 | ||
- setuptools=59.8.0=py37h89c1867_1 | ||
- simplejson=3.17.6=py37h540881e_1 | ||
- six=1.16.0=pyhd3eb1b0_1 | ||
- sqlite=3.32.3=hcee41ef_1 | ||
- star=2.6.1b=0 | ||
- star-fusion=1.5.0=0 | ||
- tbb=2020.2=h4bd325d_4 | ||
- tk=8.6.12=h27826a3_0 | ||
- typing_extensions=4.4.0=pyha770c72_0 | ||
- wget=1.20.3=ha56f1ee_1 | ||
- wheel=0.37.1=pyhd8ed1ab_0 | ||
- xz=5.2.6=h166bdaf_0 | ||
- zipp=3.9.0=pyhd8ed1ab_0 | ||
- zlib=1.2.12=h166bdaf_4 | ||
prefix: conda_env/ |
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