Commit f0654aaa authored by Blaise Li's avatar Blaise Li
Browse files

Add pip freeze from singularity container.

parent 2cc3fa8d
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
......@@ -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
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment