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Fix bioconductor package installation.
author mvdbeek
date Wed, 03 Dec 2014 01:47:58 +0100
parents 5b930e77b1f3
children de4889098f45
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2:5b930e77b1f3 3:477eac6c4cea
23 23
24 RUN easy_install pip 24 RUN easy_install pip
25 25
26 RUN pip install numpy pysam tornado matplotlib pip pandas ipython rpy2 26 RUN pip install numpy pysam tornado matplotlib pip pandas ipython rpy2
27 27
28 RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite("DESeq", "DESeq2", "edgeR", "EDASeq")' 28 RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite(c("DESeq", "DESeq2", "edgeR", "EDASeq"))'
29 RUN Rscript -e 'install.packages(c("latticeExtra", "ggplot2", "reshape", "gridExtra"), dependencies=TRUE, repos="http://cran.us.r-project.org")' 29 RUN Rscript -e 'install.packages(c("latticeExtra", "ggplot2", "reshape", "gridExtra"), dependencies=TRUE, repos="http://cran.us.r-project.org")'
30 30
31 #add galaxy user (could be any username). 31 #add galaxy user (could be any username).
32 #1001 will be replaced by the actual user id of the system user 32 #1001 will be replaced by the actual user id of the system user
33 #executing the galaxy tool, so that file write operations are possible. 33 #executing the galaxy tool, so that file write operations are possible.