From 795c27e3de1e2e2946d65816a05cddcac6b88bcc Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Wed, 29 Jan 2020 11:46:19 +0100
Subject: [PATCH] Install dependencies using requirements.txt
---
singularity/run_pipeline.def | 29 +++++++++++++++--------------
1 file changed, 15 insertions(+), 14 deletions(-)
diff --git a/singularity/run_pipeline.def b/singularity/run_pipeline.def
index 62205cb..b1ec5e1 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
--
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