Add pip freeze from singularity container.

requirements.txt

+alabaster==0.7.12
+appdirs==1.4.3
+attrs==19.3.0
+Babel==2.8.0
+# Editable install with no version control (bam25prime==0.1)
+-e /usr/local/lib/python3.7/site-packages
+beautifulsoup4==4.8.2
+bs4==0.0.1
+certifi==2019.11.28
+cffi==1.13.2
+chardet==3.0.4
+ConfigArgParse==1.0
+cycler==0.10.0
+Cython==0.29.14
+cytoolz==0.10.1
+datrie==0.8
+decorator==4.4.1
+deepTools==3.3.2
+deeptoolsintervals==0.1.9
+docutils==0.16
+gitdb2==2.0.6
+GitPython==3.0.5
+html5lib==1.0.1
+husl==4.0.3
+idna==2.8
+imagesize==1.2.0
+importlib-metadata==1.4.0
+ipython-genutils==0.2.0
+Jinja2==2.10.3
+joblib==0.14.1
+jsonschema==3.2.0
+jupyter-core==4.6.1
+kiwisolver==1.1.0
+libcelegans==0.1
+# Editable install with no version control (libdeseq==0.2)
+-e /usr/local/lib/python3.7/site-packages
+# Editable install with no version control (libhts==0.2)
+-e /usr/local/lib/python3.7/site-packages
+libreads==0.2
+# Editable install with no version control (libsmallrna==0.2)
+-e /usr/local/lib/python3.7/site-packages
+# Editable install with no version control (libworkflows==0.2)
+-e /usr/local/lib/python3.7/site-packages
+mappy==2.17
+MarkupSafe==1.1.1
+matplotlib==3.1.2
+more-itertools==8.1.0
+nbformat==5.0.4
+networkx==2.4
+numpy==1.18.1
+numpydoc==0.9.2
+packaging==20.1
+pandas==0.25.3
+paraccumulators==0.1
+plotly==4.5.0
+pluggy==0.13.1
+psutil==5.6.7
+py==1.8.1
+py2bit==0.3.0
+pybedtools==0.8.0
+pyBigWig==0.3.17
+pybind11==2.4.3
+pycparser==2.19
+Pygments==2.5.2
+pyparsing==2.4.6
+pyrsistent==0.15.7
+pysam==0.15.4
+pytest==5.3.4
+python-dateutil==2.8.1
+pytz==2019.3
+PyYAML==5.3
+-e git+https://bioinfo_utils:KU13FfM3kLyeCrWpD2ZG@gitlab.pasteur.fr/bli/qaf_demux.git@bdf4b407bbf3f8be5149e49ac4cfcc05302ab1dc#egg=qaf_demux&subdirectory=../../qaf_demux/Python
+ratelimiter==1.2.0.post0
+requests==2.22.0
+retrying==1.3.3
+rpy2==3.2.5
+scikit-learn==0.22.1
+scipy==1.4.1
+seaborn==0.10.0
+simplegeneric==0.8.1
+six==1.14.0
+smmap2==2.0.5
+snakemake==5.10.0
+# Editable install with no version control (snakemake-wrappers==0.3)
+-e /usr/local/lib/python3.7/site-packages
+snowballstemmer==2.0.0
+soupsieve==1.9.5
+Sphinx==2.3.1
+sphinxcontrib-applehelp==1.0.1
+sphinxcontrib-devhelp==1.0.1
+sphinxcontrib-htmlhelp==1.0.2
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.2
+sphinxcontrib-serializinghtml==1.1.3
+toolz==0.10.0
+toposort==1.5
+traitlets==4.3.3
+tzlocal==2.0.0
+urllib3==1.25.8
+wcwidth==0.1.8
+webencodings==0.5.1
+wrapt==1.11.2
+zipp==2.1.0

singularity/run_pipeline.def

@@ -22,7 +22,7 @@ Stage: build-haskell
 	has_haskell_install=$(find . -name install.sh -print | xargs dirname | grep "Haskell")
 	for dir in ${has_haskell_install}
 	do
-		(cd ${dir} && grep "local" install.sh && ./install.sh)
+	    (cd ${dir} && grep "local" install.sh && ./install.sh)
 	done
 
 Bootstrap:docker
@@ -82,17 +82,14 @@ 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
+	python3.7 -m pip install --upgrade pip
+	# Needs to install before custom pybedtools
+	# python3.7 -m pip install pysam
 	# 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
-	# Getting custom pybedtools that includes *.h headers
-	#git clone https://github.com/blaiseli/pybedtools.git
-	#cd pybedtools
-	#git checkout fix_missing_headers
-	#/usr/bin/env python3 setup.py cythonize
-	#/usr/bin/env python3 -m pip install .
 	# Getting the workflows
 	cd /usr/local/src
 	#git clone --recurse-submodules https://gitlab+deploy-token-75:sakyTxfe-PxPHDwqsoGm@gitlab.pasteur.fr/bli/bioinfo_utils.git
@@ -105,12 +102,12 @@ From:python:3.7-buster
 	# apt install -y gfortran
 	for dir in ${has_requirements}
 	do
-		(cd ${dir} && pip install -r requirements.txt)
+	    (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)
+	    (cd ${dir} && ./install.sh)
 	done
 
 %environment