Mercurial > repos > mvdbeek > docker_toolfactory
comparison Dockerfile @ 0:0fa46413d0d9 draft
planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
| author | mvdbeek |
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| date | Sat, 03 Oct 2015 08:34:39 -0400 |
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| -1:000000000000 | 0:0fa46413d0d9 |
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| 1 # Toolfactory image | |
| 2 # | |
| 3 # VERSION 0.2 | |
| 4 # This Dockerfile is the base system for executing scripts by the DockerToolFactory. | |
| 5 | |
| 6 FROM toolshed/requirements | |
| 7 | |
| 8 MAINTAINER Marius van den Beek, m.vandenbeek@gmail.com | |
| 9 | |
| 10 # make sure the package repository is up to date | |
| 11 ENV DEBIAN_FRONTEND noninteractive | |
| 12 | |
| 13 #add galaxy user (could be any username). | |
| 14 #1001 will be replaced by the actual user id of the system user | |
| 15 #executing the galaxy tool, so that file write operations are possible. | |
| 16 RUN adduser galaxy -u 1000 | |
| 17 | |
| 18 | |
| 19 ADD adduser.sh /usr/local/bin/adduser.sh | |
| 20 RUN adduser.sh | |
| 21 | |
| 22 RUN ulimit -n 1024 && apt-get update -qq && apt-get install -y --no-install-recommends software-properties-common && apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E084DAB9 && add-apt-repository \ | |
| 23 "deb http://cran.irsn.fr/bin/linux/ubuntu trusty/" && apt-get update -qq && apt-get upgrade && apt-get install -y r-base-core r-base-dev \ | |
| 24 adduser zlib1g-dev python-virtualenv python-pip libfreetype6-dev bedtools wget curl \ | |
| 25 libcurl4-openssl-dev libssl-dev libreadline-dev libxml2-dev samtools liblzma-dev \ | |
| 26 libpcre3-dev libbz2-dev | |
| 27 | |
| 28 RUN pip install numpy pysam tornado matplotlib pycurl pip pandas ipython rpy2 | |
| 29 | |
| 30 #RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite("DESeq", "DESeq2", "edgeR", "EDASeq")' | |
| 31 #RUN Rscript -e 'install.packages(c("latticeExtra", "ggplot2", "reshape", "gridExtra"), dependencies=TRUE, repos="http://cran.us.r-project.org")' | |
| 32 | |
| 33 RUN mkdir /home/galaxy/job_working_directory | |
| 34 WORKDIR /home/galaxy/job_working_directory | |
| 35 USER galaxy | |
| 36 | |
| 37 #ENTRYPOINT chown -R galaxy /home/galaxy/ && su - galaxy | |
| 38 CMD /bin/bash |