diff --git a/src/.docker_modules/emase/0.10.16/Dockerfile b/src/.docker_modules/emase/0.10.16/Dockerfile index 94c663fdbec5f5c6f0761d5523b5530c2d34414c..9fd749384558b5ca31179378a4682f1f3ff8a304 100644 --- a/src/.docker_modules/emase/0.10.16/Dockerfile +++ b/src/.docker_modules/emase/0.10.16/Dockerfile @@ -1,27 +1,13 @@ -FROM python:2.7 +FROM conda/miniconda2 MAINTAINER Laurent Modolo ENV EMASE_VERSION=0.10.16 - -RUN -apt-get update \ - && apt-get install -y python-h5py libhdf5-dev \ - && pip install tables \ - && pip install scipy \ - && pip install pysam \ - && pip install numpy==1.8.2 \ - && pip install numexpr==2.3.1 \ - && pip install cython>=0.13 \ - && pip install tables==3.1.0 \ - && pip install emase==${EMASE_VERSION} - -pip install numpy==1.8.2 -pip install numexpr==2.3.1 -pip install scipy==0.13.3 -pip install pysam>=0.6 -pip install cython>=0.13 -pip install tables -pip install biopython>=1.63 - -CMD ["bash"] - +RUN conda init \ +&& conda config --add channels r \ +&& conda config --add channels bioconda \ +&& conda create -y -n emase jupyter +SHELL ["conda", "run", "-n", "emase", "/bin/bash", "-c"] +RUN conda install -y -c kbchoi emase \ +&& echo "conda activate emase" >> /root/.bashrc + +ENV PATH /usr/local/envs/emase/bin:/usr/local/condabin:$PATH