Commit 795c27e3 authored by Blaise Li's avatar Blaise Li
Browse files

Install dependencies using requirements.txt

parent daef0163
......@@ -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
......
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