Install dependencies using requirements.txt

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