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Dockerfile refactoring
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0x00b1 committed Oct 28, 2015
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6 changes: 6 additions & 0 deletions .travis.yml
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services:
- docker
script:
- make
- make test
sudo: required
101 changes: 86 additions & 15 deletions Dockerfile
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FROM centos:centos6

# See cellprofiler.org/linux.shtml

COPY cellprofiler.repo /etc/yum.repos.d/
RUN yum install -y cellprofiler-2.1.1

RUN useradd cellprofiler
USER cellprofiler
ENV HOME /home/cellprofiler
WORKDIR /home/cellprofiler

ENTRYPOINT ["cellprofiler", "-r", "-c"]
CMD ["-h"]
# Use -p filename for execution
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# - [ BROAD‘15 ] -
# -0x00B1 [05/06/84]
FROM ubuntu:14.04
RUN apt-get -y update && \
apt-get -y upgrade && \
apt-get -y install \
cython \
git \
openjdk-7-jdk \
python-h5py \
python-imaging \
python-libtiff \
python-lxml \
python-matplotlib \
python-mysqldb \
python-numpy \
python-pandas \
python-pip \
python-scipy \
python-skimage \
python-sklearn \
python-vigra \
python-wxgtk2.8 \
python-zmq \
xvfb
WORKDIR /usr/local/src
RUN git clone https://github.com/CellProfiler/CellProfiler.git
WORKDIR /usr/local/src/CellProfiler
RUN pip install \
--requirement \
requirements.txt
RUN pip install \
--editable \
git+https://github.com/CellH5/cellh5.git#egg=cellh5 \
--upgrade
RUN python external_dependencies.py
RUN python CellProfiler.py --build-and-exit
ENTRYPOINT ["python", "CellProfiler.py", "--run", "--run-headless"]
CMD ["--help"]
41 changes: 41 additions & 0 deletions Makefile
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SVN = http://cellprofiler.org/svnmirror/ExampleImages/ExampleHumanImages

.PHONY: input
input:
mkdir -p $@

output:
mkdir -m 777 -p $@

ExampleHuman.cppipe:
curl -O ${SVN}/ExampleHuman.cppipe

input/ExampleHuman.cppipe: ExampleHuman.cppipe
mv $< $@

AS_09125_050116030001_D03f00d0.tif:
curl -O ${SVN}/$@

input/AS_09125_050116030001_D03f00d0.tif: AS_09125_050116030001_D03f00d0.tif
mv $< $@

AS_09125_050116030001_D03f00d1.tif: AS_09125_050116030001_D03f00d1.tif
curl -O ${SVN}/$@

input/AS_09125_050116030001_D03f00d1.tif: AS_09125_050116030001_D03f00d1.tif
mv $< $@

AS_09125_050116030001_D03f00d2.tif:
curl -O ${SVN}/$@

input/AS_09125_050116030001_D03f00d2.tif: AS_09125_050116030001_D03f00d2.tif
mv $< $@

input/filelist.txt: input/AS_09125_050116030001_D03f00d0.tif input/AS_09125_050116030001_D03f00d1.tif input/AS_09125_050116030001_D03f00d2.tif
echo 'file:///input/AS_09125_050116030001_D03f00d0.tif' >> $@
echo 'file:///input/AS_09125_050116030001_D03f00d1.tif' >> $@
echo 'file:///input/AS_09125_050116030001_D03f00d2.tif' >> $@

.PHONY: test
test: input output input/filelist.txt input/ExampleHuman.cppipe
docker run --volume=`pwd`/input:/input --volume=`pwd`/output:/output cellprofiler --image-directory=/input --output-directory=/output --pipeline=/input/ExampleHuman.cppipe --file-list=/input/filelist.txt
5 changes: 5 additions & 0 deletions README.markdown
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# docker

$ make

$ make test
18 changes: 0 additions & 18 deletions README.md
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12 changes: 0 additions & 12 deletions cellprofiler-avoid-blank-libdir-for-libjvm.diff
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11 changes: 0 additions & 11 deletions cellprofiler-frozen.diff
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5 changes: 0 additions & 5 deletions cellprofiler.repo
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11 changes: 0 additions & 11 deletions threshold.diff
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