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build: docker file and small readme update

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amcpherson committed Mar 4, 2019
1 parent eeb5159 commit cf20128764e60925e3dc1722ec626b2fe3a9ee3b
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  1. +13 −0 Dockerfile
  2. +11 −0 README.md
@@ -0,0 +1,13 @@
FROM continuumio/miniconda
ARG app_version

RUN conda config --add channels https://conda.anaconda.org/dranew && conda config --add channels bioconda
RUN conda install destruct==$app_version
RUN conda install openssl=1.0
RUN mkdir -p /root/.config/matplotlib
RUN echo "backend : Agg" > /root/.config/matplotlib/matplotlibrc

ENV NAME destruct

ENTRYPOINT ["destruct"]

@@ -171,3 +171,14 @@ To run a script on a cluster with qsub/qstat, add the following command line opt
Often a call to qsub requires specific command line parameters to request the correct queue, and importantly to request the correct amount of memory. To allow correct calls to qsub, use the `--nativespec` command line option, and use the placeholder `{mem}` which will be replaced by the amount of memory (in gigabytes) required for each job launched with qsub. For example, to use qsub, and request queue `all.q` and set the `mem_free` to the required memory, add the following command line options:

--submit asyncqsub --nativespec "-q all.q -l mem_free={mem}G"

# Build

## Docker builds

To build a destruct docker image, for instance version v0.4.13, run the following docker command:

docker build --build-arg app_version=0.4.13 -t amcpherson/destruct .
docker push amcpherson/destruct:0.4.13


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