Commit 3a505aeb authored by Blaise Li's avatar Blaise Li
Browse files

Install numpy and cython later.

Instead of installing them in the base container, they are installed
together with the workflows, using the versions from the requirements
file.
parent 943f2543
......@@ -78,7 +78,11 @@ From:workflows_base.sif
cd bioinfo_utils
WORKFLOWS_VERSION=$(git log | head -1 | cut -d " " -f2)
# It seems pybedtools does not auto-install it
pip install Cython
grep Cython requirements.txt > requirements_Cython.txt
pip install -r requirements_Cython.txt
# Should be installed before pyBedTools and pyBigWig for them to have numpy support
grep numpy requirements.txt > requirements_numpy.txt
pip install -r requirements_numpy.txt
#pip install -r requirements.txt --use-deprecated=legacy-resolver
pip install -r requirements.txt
prog="Python packages"
......
......@@ -159,8 +159,6 @@ From:python:3.7-buster
pip3 install --upgrade pip
# Useful for experimenting in shell mode
pip3 install ipython
# Should be installed before pyBedTools and pyBigWig for them to have numpy support
pip3 install numpy
# Needs to install before custom pybedtools
# pip3 install pysam
# To get scipy properly built as requirement:
......
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