Mercurial > repos > fubar > differential_count_models
diff tool_dependencies.xml @ 48:1c6c7e481be7 draft
removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
| author | fubar |
|---|---|
| date | Mon, 23 Dec 2013 17:14:14 -0500 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Dec 23 17:14:14 2013 -0500 @@ -0,0 +1,50 @@ +<?xml version="1.0"?> +<tool_dependency> +<!-- + this will not compile for me - it thinks we have autoscaling on + - so we need libopenblas-base installed on all nodes...grrr + <package name="atlas" version="3.11.11"> + <repository name='package_atlas_3_11' owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + </package> + and we need this added to the set_environment section below too + <repository name="package_atlas_3_11" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/"> + <package name="atlas" version="3.11.11" /> + </repository> +--> + <package name="r3" version="3.0.1"> + <repository changeset_revision="6e89ec508745" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + </package> + <package name="ghostscript" version="9.07"> + <repository changeset_revision="7245d8573fca" name="package_ghostscript_9_07" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + </package> + <package name="graphicsmagick" version="1.3.18"> + <repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + </package> + <package name="biocbasics" version="2.12"> + <install version="1.0"> + <actions> + <action type="set_environment_for_install"> + <repository changeset_revision="6e89ec508745" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/"> + <package name="r3" version="3.0.1" /> + </repository> + </action> + <action type="make_directory">$INSTALL_DIR</action> + <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" > $INSTALL_DIR/runme.R</action> + <action type="shell_command">echo "installme=c('edgeR','limma','DESeq','DESeq2')" >> $INSTALL_DIR/runme.R</action> + <action type="shell_command">echo "biocLite()" >> $INSTALL_DIR/runme.R</action> + <action type="shell_command">echo "biocLite(installme)" >> $INSTALL_DIR/runme.R</action> + <action type="shell_command">echo "install.packages(c('stringr','gplots'),dependencies=T,repos='http://cran.us.r-project.org')" >> $INSTALL_DIR/runme.R</action> + <action type="shell_command">echo "quit(save='no')" >> $INSTALL_DIR/runme.R</action> + <action type="shell_command"> export PATH=$PATH && export R_HOME=$R_HOME && export R_LIBS=$R_LIBS && R CMD BATCH $INSTALL_DIR/runme.R </action> + </actions> + </install> + <readme>Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick + (replaces imagemagick) and ghostscript for compressing R's bloated pdfs + It's clunky but this is the most convenient way I could get anything installed into the package_r3 + Note we use cran at fred hutch since no fastest mirror thingy + copyright ross lazarus last updated december 2013 ross stop lazarus at gmail stop com + License to use this source (dependencies have their own obligations) + is made available to you under the terms of the LGPL + </readme> + </package> +</tool_dependency>