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 ...@@ -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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