Commit 7f6056dc authored by Blaise Li's avatar Blaise Li
Browse files

Fix scipy build issue.

parent 1e37c6ef
......@@ -18,4 +18,4 @@ install: run_pipeline
# Should depend on the rest of the repository.
run_pipeline: run_pipeline.def
sudo singularity build run_pipeline run_pipeline.def
nohup sh -c "yes | sudo singularity build run_pipeline run_pipeline.def > build.err 2>&1" &
......@@ -80,6 +80,8 @@ From:python:3.7-buster
# To avoid using python things installed in the HOME of root
# (that will be mounted during singularity build)
export PYTHONNOUSERSITE=1
# To get scipy properly built as requirement:
python3.7 -m pip install pybind11
# Needed to manually cythonize custom pybedtools before installing it
#/usr/bin/env python3 -m pip install Cython
#/usr/bin/env python3 -m pip install --global-option="cythonize" git+https://github.com/blaiseli/pybedtools.git@fix_missing_headers
......@@ -96,6 +98,9 @@ From:python:3.7-buster
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)
......
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