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cellprofiler_315.rec
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cellprofiler_315.rec
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Bootstrap: docker
From: ubuntu:16.04
%labels
version="3.1.5"
%post
# define volumes
# VOLUME /mnt/data /mnt/img
# # add apt mirrors
echo "deb mirror://mirrors.ubuntu.com/mirrors.txt xenial main restricted universe multiverse" > /etc/apt/sources.list && \
echo "deb mirror://mirrors.ubuntu.com/mirrors.txt xenial-updates main restricted universe multiverse" >> /etc/apt/sources.list && \
echo "deb mirror://mirrors.ubuntu.com/mirrors.txt xenial-security main restricted universe multiverse" >> /etc/apt/sources.list
# update system
apt-get update && apt-get upgrade -y
# install tools
apt-get install -y \
build-essential=12.1ubuntu2 \
cython=0.23.4-0ubuntu5 \
git \
libmysqlclient-dev \
libhdf5-dev=1.8.16+docs-4ubuntu1.1 \
libxml2-dev \
libxslt1-dev \
libatk-adaptor \
libgail-common \
libcanberra-gtk-module \
openjdk-8-jdk \
libssl-dev \
python-dev=2.7.12-1~16.04 \
python-pip=8.1.1-2ubuntu0.4 \
python-h5py=2.6.0-1 \
python-matplotlib=1.5.1-1ubuntu1 \
python-mysqldb=1.3.7-1build2 \
python-scipy=0.17.0-1 \
python-vigra=1.10.0+dfsg-11ubuntu2 \
python-wxgtk3.0=3.0.2.0+dfsg-1build1
pip install pip==20.0.1
# get CellProfiler
cd /usr/local/src
git clone https://github.com/CellProfiler/CellProfiler.git && cd CellProfiler && git checkout tags/v3.1.5
# version specific python packages
pip install pytest==3.10.0
pip install \
centrosome==1.1.5 \
certifi==2018.10.15 \
chardet==3.0.4 \
cloudpickle==0.6.1 \
contextlib2==0.5.5 \
cycler==0.10.0 \
Cython==0.23.4 \
dask==0.18.0 \
decorator==4.3.0 \
deprecation==2.0.6 \
docutils==0.14 \
funcsigs==1.0.2 \
future==0.17.1 \
futures==3.2.0 \
h5py==2.6.0 \
idna==2.7 \
inflect==1.0.1 \
javabridge==1.0.18 \
jmespath==0.9.3 \
joblib==0.13.0 \
kiwisolver==1.0.1 \
mahotas==1.4.5 \
matplotlib==2.2.3 \
more-itertools==4.3.0 \
mysqlclient==1.3.13 \
networkx==2.2 \
numpy==1.11.0 \
packaging==18.0 \
pathlib2==2.3.2 \
Pillow==5.3.0 \
pluggy==0.8.0 \
prokaryote==2.4.0 \
py==1.7.0 \
pyparsing==2.0.3 \
python-bioformats==1.4.0 \
python-dateutil==2.4.2 \
pytz==2014.10 \
PyWavelets==1.0.1 \
pyzmq==15.3.0 \
raven==6.9.0 \
requests==2.20.0 \
s3transfer==0.1.13 \
scandir==1.9.0 \
scikit-image==0.14.1 \
scikit-learn==0.20.0 \
scipy==0.17.0 \
six==1.10.0 \
subprocess32==3.5.3 \
toolz==0.9.0 \
urllib3==1.24.1 \
wxPython==3.0.2.0 \
wxPython-common==3.0.2.0 \
# install CellProfiler
cd /usr/local/src/CellProfiler
cd /usr/local/src/CellProfiler ; pip install --editable .
pip install numpy==1.11.0
%runscript
cd /usr/local/src/CellProfiler
exec cellprofiler "$@"
%startscript
cd /usr/local/src/CellProfiler
exec cellprofiler "$@"