Commit 0a9e267f authored by Damien VINTACHE's avatar Damien VINTACHE
Browse files

les environnements conda utilisés dans les règles snakemake sont créés à partir des fichiers yml

parent e085f3dc
......@@ -24,7 +24,7 @@ echo "=== configure the pipeline environement ==="
# Run pipeline
echo "=== run the pipeline ==="
echo "number of snakemake jobs : $SNAKEMAKE_JOBS"
snakemake -rp --jobs ${2} --config projf="CONFIG/project.json" reff="CONFIG/references.json" conff="CONFIG/config.json" --use-conda
snakemake -rp --jobs ${2} --latency-wait 60 --config projf="CONFIG/project.json" reff="CONFIG/references.json" conff="CONFIG/config.json" --use-conda
# check the result
echo "=== check the result ==="
......
......@@ -21,7 +21,7 @@ rm -f ${1}/miniconda.sh
export PATH=${1}/miniconda/bin:$PATH
# Install of the exome environment
/bin/bash ${1}/CONDA/createEnv.sh
# /bin/bash ${1}/CONDA/createEnv.sh
# List environment
echo "=== list available conda environments ==="
......
name: rnaSeqQuantif
channels:
- ostrokach
- dougal
- r
- bird
- conda-forge
- bioconda
- defaults
dependencies:
- bcftools=1.8=h4da6232_3
- bcftools=1.9=h4da6232_0
- cutadapt=1.16=py36_2
- fastqc=0.11.7=4
- filechunkio=1.6=py36_0
......@@ -16,62 +13,59 @@ dependencies:
- htseq=0.9.1=py36h24bf2e0_1
- htslib=1.7=0
- libdeflate=1.0=h470a237_0
- multiqc=1.6a0=py36h24bf2e0_2
- multiqc=1.6=py36h24bf2e0_0
- perl-threaded=5.22.0=13
- prinseq=0.20.4=2
- pyasn1-modules=0.0.5=py36_0
- pygraphviz=1.3.1=py36_0
- pysam=0.14.1=py36hae42fb6_1
- pysftp=0.2.9=py36_0
- rsa=3.1.4=py36_0
- samtools=1.7=1
- simplejson=3.8.1=py36_0
- snakemake=5.2.0=py36_0
- star=2.6.0c=1
- snakemake=4.6.0=py36_0
- star=2.6.1a=1
- urllib3=1.12=py36_0
- xopen=0.3.2=py_1
- xopen=0.3.2=py36_0
- aioeasywebdav=2.2.0=py36_0
- aiohttp=3.3.2=py36h14c3975_0
- aiohttp=3.3.2=py36h470a237_1
- appdirs=1.4.3=py_1
- asn1crypto=0.24.0=py_1
- asn1crypto=0.24.0=py36_2
- async-timeout=3.0.0=py36_0
- attrs=18.1.0=py_1
- boto3=1.7.58=py_0
- botocore=1.10.58=py_0
- blas=1.1=openblas
- boto3=1.7.78=py_0
- botocore=1.10.78=py_0
- bzip2=1.0.6=h470a237_2
- ca-certificates=2018.4.16=0
- cachetools=2.0.1=py_0
- cairo=1.14.10=0
- certifi=2018.4.16=py36_0
- cffi=1.11.5=py36_0
- chardet=3.0.4=py36_2
- ca-certificates=2018.8.13=ha4d7672_0
- cachetools=2.1.0=py_0
- certifi=2018.8.13=py36_0
- cffi=1.11.5=py36h5e8e0c9_1
- chardet=3.0.4=py36_3
- click=6.7=py_1
- colormath=3.0.0=py_2
- configargparse=0.13.0=py_1
- cryptography=2.2.1=py36hdffb7b8_1
- curl=7.60.0=0
- cryptography=2.3.1=py36hdffb7b8_0
- cryptography-vectors=2.3.1=py36_0
- curl=7.61.0=h93b3f91_1
- cycler=0.10.0=py_1
- dbus=1.13.0=h3a4f0e9_0
- decorator=4.3.0=py_0
- docutils=0.14=py36_0
- dropbox=7.3.1=py36_0
- expat=2.2.5=hfc679d8_1
- fontconfig=2.12.6=0
- freetype=2.8.1=0
- future=0.16.0=py36_0
- fontconfig=2.13.0=h65d0f4c_5
- freetype=2.9.1=h6debe1e_0
- future=0.16.0=py36_2
- gettext=0.19.8.1=0
- glib=2.55.0=0
- glib=2.55.0=h464dc38_2
- google-auth=1.2.1=py_0
- google-auth-httplib2=0.0.2=py36_0
- google-cloud-core=0.24.1=py36_0
- google-cloud-storage=1.1.1=py36_0
- google-resumable-media=0.0.2=py36_0
- googleapis-common-protos=1.5.3=py_1
- graphite2=1.3.11=hfc679d8_0
- graphviz=2.38.0=7
- gst-plugins-base=1.8.0=0
- gstreamer=1.8.0=1
- harfbuzz=1.7.6=0
- gst-plugins-base=1.12.5=hde13a9d_0
- gstreamer=1.12.5=h61a6719_0
- httplib2=0.11.3=py36_0
- icu=58.2=hfc679d8_0
- idna=2.7=py36_2
......@@ -79,81 +73,71 @@ dependencies:
- jinja2=2.10=py_1
- jmespath=0.9.3=py_1
- jpeg=9c=h470a237_0
- jsonschema=2.6.0=py36_1
- kiwisolver=1.0.1=py36_1
- kiwisolver=1.0.1=py36h2d50403_2
- krb5=1.14.6=0
- libffi=3.2.1=3
- libiconv=1.15=h470a237_1
- libpng=1.6.34=ha92aebf_1
- libprotobuf=3.5.2=hd28b015_1
- libffi=3.2.1=hfc679d8_4
- libgcc=7.2.0=h69d50b8_2
- libgcc-ng=7.2.0=hdf63c60_3
- libgfortran=3.0.0=1
- libiconv=1.15=h470a237_2
- libpng=1.6.35=ha92aebf_0
- libprotobuf=3.6.0=hd28b015_0
- libssh2=1.8.0=h5b517e9_2
- libtiff=4.0.9=he6b73bb_1
- libtool=2.4.6=0
- libxcb=1.13=h470a237_1
- libxml2=2.9.8=h422b904_2
- libstdcxx-ng=7.2.0=hdf63c60_3
- libuuid=2.32.1=h470a237_0
- libxcb=1.13=h470a237_2
- libxml2=2.9.8=h422b904_3
- lzstring=1.0.3=py36_0
- markdown=2.6.11=py_0
- markupsafe=1.0=py36_0
- matplotlib=2.2.2=py36_1
- mkl_fft=1.0.2=py36_0
- mkl_random=1.0.1=py36_0
- matplotlib=2.2.3=py36h8e2386c_0
- multidict=4.3.1=py36h470a237_0
- ncurses=6.1=0
- ncurses=6.1=hfc679d8_1
- networkx=2.0=py36_1
- openjdk=8.0.144=zulu8.23.0.3_1
- openssl=1.0.2o=0
- pandas=0.23.3=py36_0
- pango=1.40.14=0
- paramiko=2.4.1=py36_0
- pcre=8.41=1
- numpy=1.15.0=py36_blas_openblashd3ea46f_200
- openblas=0.2.20=8
- openjdk=8.0.144=zulu8.23.0.3_2
- openssl=1.0.2o=h470a237_1
- pandas=0.23.4=py36hf8a1672_0
- paramiko=2.1.2=py36_0
- pcre=8.41=h470a237_2
- perl=5.26.2=h470a237_0
- pigz=2.3.4=0
- pip=9.0.3=py36_0
- pixman=0.34.0=2
- pip=18.0=py36_1
- prettytable=0.7.2=py_2
- protobuf=3.5.2=py36_0
- psutil=5.4.6=py36_0
- protobuf=3.6.0=py36hfc679d8_0
- psutil=5.4.7=py36_0
- pthread-stubs=0.4=h470a237_1
- pyasn1=0.4.3=py_0
- pyasn1=0.4.4=py_0
- pycparser=2.18=py_1
- pynacl=1.1.2=py36_0
- pyparsing=2.2.0=py_1
- pyqt=5.6.0=py36h8210e8a_6
- python=3.6.6=h5001a0f_0
- python-dateutil=2.7.3=py_0
- python-irodsclient=0.7.0=py_0
- pytz=2018.5=py_0
- pyyaml=3.12=py36_1
- qt=5.6.2=7
- qt=5.6.2=hf70d934_9
- ratelimiter=1.2.0=py36_0
- readline=7.0=haf1bffa_1
- requests=2.13.0=py36_0
- s3transfer=0.1.13=py36_0
- setuptools=40.0.0=py36_0
- setuptools=40.0.0=py36_1
- sip=4.18=py36_1
- six=1.11.0=py36_1
- spectra=0.0.11=py_0
- sqlite=3.20.1=0
- tk=8.6.7=0
- tornado=5.1=py36_0
- wheel=0.31.1=py36_0
- sqlite=3.24.0=h2f33b56_0
- tk=8.6.8=0
- tornado=5.1=py36h470a237_1
- wheel=0.31.1=py36_1
- wrapt=1.10.11=py36_0
- xmlrunner=1.7.7=py_0
- xorg-libxau=1.0.8=h470a237_5
- xorg-libxdmcp=1.1.2=h470a237_6
- xz=5.2.3=0
- yaml=0.1.7=0
- xorg-libxau=1.0.8=h470a237_6
- xorg-libxdmcp=1.1.2=h470a237_7
- xz=5.2.4=h470a237_1
- yaml=0.1.7=h470a237_1
- yarl=1.2.6=py36h470a237_0
- zlib=1.2.11=h470a237_3
- bcrypt=3.1.4=py36h14c3975_0
- bz2file=0.98=py36_1
- datrie=0.7.1=py36_0
- intel-openmp=2018.0.3=0
- libgcc=7.2.0=h69d50b8_2
- libgcc-ng=7.2.0=hdf63c60_3
- libgfortran-ng=7.2.0=hdf63c60_3
- libstdcxx-ng=7.2.0=hdf63c60_3
- mkl=2018.0.3=1
- numpy=1.14.2=py36hdbf6ddf_1
- python=3.6.4=hc3d631a_1
- readline=7.0=ha6073c6_4
- gzip=1.7=1
prefix: /home/vintache-d/miniconda3/envs/rnaSeqQuantif
prefix: /home/vintache-d/RNAseq_quantif_pipeline/miniconda/envs/rnaSeqQuantif
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment