From aaa243c8858088e85c3e308c1c57b5d11d00cbad Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 23 Sep 2021 12:50:32 +0200
Subject: [PATCH] emase: working Dockerfile for emase to install it from conda
---
src/.docker_modules/emase/0.10.16/Dockerfile | 34 ++++++--------------
1 file changed, 10 insertions(+), 24 deletions(-)
diff --git a/src/.docker_modules/emase/0.10.16/Dockerfile b/src/.docker_modules/emase/0.10.16/Dockerfile
index 94c663fd..9fd74938 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
--
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