diff --git a/singularity/run_pipeline.def b/singularity/run_pipeline.def index 62205cb8f7cd02d074a9be44a192a442851821ed..b1ec5e1e5241eb27215f74b853e92947a9eae72b 100644 --- a/singularity/run_pipeline.def +++ b/singularity/run_pipeline.def @@ -95,20 +95,21 @@ From:python:3.7-buster #git clone --recurse-submodules https://gitlab+deploy-token-75:sakyTxfe-PxPHDwqsoGm@gitlab.pasteur.fr/bli/bioinfo_utils.git git clone https://gitlab+deploy-token-75:sakyTxfe-PxPHDwqsoGm@gitlab.pasteur.fr/bli/bioinfo_utils.git cd bioinfo_utils - git submodule update --init --remote --merge - has_requirements=$(find . -name requirements.txt -print | xargs dirname) - # Needed for scipy (https://stackoverflow.com/a/58534155/1878788) - # No, does not solve the issue... - # apt install -y gfortran - for dir in ${has_requirements} - do - (cd ${dir} && pip install -r requirements.txt) - done - has_install=$(find . -name install.sh -print | xargs dirname | grep -v "Nim" | grep -v "Haskell") - for dir in ${has_install} - do - (cd ${dir} && ./install.sh) - done + pip install -r requirements.txt + #git submodule update --init --remote --merge + #has_requirements=$(find . -name requirements.txt -print | xargs dirname) + ## Needed for scipy (https://stackoverflow.com/a/58534155/1878788) + ## No, does not solve the issue... + ## apt install -y gfortran + #for dir in ${has_requirements} + #do + # (cd ${dir} && pip install -r requirements.txt) + #done + #has_install=$(find . -name install.sh -print | xargs dirname | grep -v "Nim" | grep -v "Haskell") + #for dir in ${has_install} + #do + # (cd ${dir} && ./install.sh) + #done %environment export LC_ALL=C