From f512f1e5dfaa3a0f2444e7a04b9122896e0529af Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 7 Oct 2021 16:20:58 +0200
Subject: [PATCH] docker: bioconvert switch to conda install
---
src/.docker_modules/bioconvert/0.4.3/Dockerfile | 17 +++++++++++++----
1 file changed, 13 insertions(+), 4 deletions(-)
diff --git a/src/.docker_modules/bioconvert/0.4.3/Dockerfile b/src/.docker_modules/bioconvert/0.4.3/Dockerfile
index e2863bff..eb4dc3d0 100644
--- a/src/.docker_modules/bioconvert/0.4.3/Dockerfile
+++ b/src/.docker_modules/bioconvert/0.4.3/Dockerfile
@@ -1,7 +1,16 @@
-FROM python:3.9-slim
+FROM conda/miniconda3
+MAINTAINER Laurent Modolo
ENV BIOCONVERT_VERSION="0.4.3"
+RUN conda init \
+&& conda config --add channels r \
+&& conda config --add channels defaults \
+&& conda config --add channels conda-forge \
+&& conda config --add channels bioconda \
+&& conda create -y -n bioconvert
+SHELL ["conda", "run", "-n", "bioconvert", "/bin/bash", "-c"]
+RUN conda install bioconvert \
+&& echo "conda activate bioconvert" >> /root/.bashrc
+RUN apt update && apt install -y procps
-RUN apt update && apt install -y procps gcc zlib1g-dev && pip3 install bioconvert==${BIOCONVERT_VERSION}
-
-CMD [ "bash" ]
+ENV PATH /usr/local/envs/bioconvert/bin:/usr/local/condabin:$PATH
--
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