Merge pull request #30 from TRON-Bioinformatics/dev

Dev

Docker/Dockerfile

@@ -5,23 +5,25 @@ RUN DEBIAN_FRONTEND="noninteractive" apt-get install -y software-properties-comm
 
 COPY ./code/ /code/
 
-RUN curl -O https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh
-RUN bash Miniconda2-latest-Linux-x86_64.sh -b -p /code/miniconda2
-RUN rm Miniconda2-latest-Linux-x86_64.sh
-ENV PATH /code/miniconda2/bin:$PATH
+RUN curl -O https://repo.anaconda.com/miniconda/Miniconda3-py37_4.12.0-Linux-x86_64.sh
+RUN bash Miniconda3-py37_4.12.0-Linux-x86_64.sh -b -p /code/miniconda3
+RUN rm Miniconda3-py37_4.12.0-Linux-x86_64.sh
+ENV PATH /code/miniconda3/bin:$PATH
 RUN conda update conda
 RUN conda update --all
 RUN conda install -y -c anaconda pandas=0.24.0
 RUN conda install -y -c conda-forge python-lzo=1.12 python-xxhash=1.4.3 biopython=1.73
 RUN conda install -y -c bioconda pysam=0.15.2 star=2.6.1b samtools=1.9.0 mapsplice=2.2.1
-RUN conda install -y -c bioconda star-fusion=1.5.0 bowtie=1.1.2
+RUN conda install -y -c bioconda star-fusion=1.5.0 bowtie=1.2.3
 RUN conda install -y -c bioconda bowtie2=2.3.4.3
 RUN conda install -y -c bioconda bx-python=0.8.2 gffutils=0.10.1
 RUN conda install -y -c bioconda fastqc=0.11.9
 RUN conda install -y -c bioconda perl-parallel-forkmanager=2.02
 RUN conda clean -ay
+RUN conda create --name py27 python=2.7
+RUN conda install --name py27 -y -c conda-forge biopython=1.73
 
-# These commands should install R-4.2.0
+# These commands should install R-4.2.1
 # Maybe try to specify version to make installation more stable
 
 RUN wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc

_version.py

@@ -0,0 +1,2 @@
+__version_info__ = (1, 3, 7)
+__version__ = '.'.join(map(str, __version_info__))

build_env.sh.sample

@@ -1,16 +1,7 @@
 #!/bin/bash
 
-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
 
-module purge
-
-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/

config.ini.docker

@@ -5,11 +5,10 @@
 # 4) To whom shall slurm mails be sent to (receiver)
 
 [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
@@ -45,6 +44,9 @@ summary = 1,16
 
 # 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
@@ -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

config.ini.sample

@@ -5,7 +5,6 @@
 # 4) To whom shall slurm mails be sent to (receiver)
 
 [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

environment.yml

@@ -0,0 +1,165 @@
+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/