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Blaise LI
bioinfo_utils
Commits
795c27e3
Commit
795c27e3
authored
5 years ago
by
Blaise Li
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Install dependencies using requirements.txt
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daef0163
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singularity/run_pipeline.def
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795c27e3
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@@ -95,20 +95,21 @@ From:python:3.7-buster
...
@@ -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 --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
git clone https://gitlab+deploy-token-75:sakyTxfe-PxPHDwqsoGm@gitlab.pasteur.fr/bli/bioinfo_utils.git
cd bioinfo_utils
cd bioinfo_utils
git submodule update --init --remote --merge
pip install -r requirements.txt
has_requirements=$(find . -name requirements.txt -print | xargs dirname)
#git submodule update --init --remote --merge
# Needed for scipy (https://stackoverflow.com/a/58534155/1878788)
#has_requirements=$(find . -name requirements.txt -print | xargs dirname)
# No, does not solve the issue...
## Needed for scipy (https://stackoverflow.com/a/58534155/1878788)
# apt install -y gfortran
## No, does not solve the issue...
for dir in ${has_requirements}
## apt install -y gfortran
do
#for dir in ${has_requirements}
(cd ${dir} && pip install -r requirements.txt)
#do
done
# (cd ${dir} && pip install -r requirements.txt)
has_install=$(find . -name install.sh -print | xargs dirname | grep -v "Nim" | grep -v "Haskell")
#done
for dir in ${has_install}
#has_install=$(find . -name install.sh -print | xargs dirname | grep -v "Nim" | grep -v "Haskell")
do
#for dir in ${has_install}
(cd ${dir} && ./install.sh)
#do
done
# (cd ${dir} && ./install.sh)
#done
%environment
%environment
export LC_ALL=C
export LC_ALL=C
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