Mercurial > repos > fubar > differential_count_models
view tool_dependencies.xml @ 94:9414bbf5579b draft
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author | fubar |
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date | Sun, 02 Mar 2014 22:32:01 -0500 |
parents | 34ef458b7fd9 |
children | 8c96a2d95436 |
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<?xml version="1.0"?> <tool_dependency> <package name="ghostscript" version="9.07"> <repository changeset_revision="10222a7db54c" name="package_ghostscript_9_07" owner="fubar" 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="r303" version="3.0.3"> <repository changeset_revision="4c934f6b342e" name="package_r303" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> </package> <package name="biocbasics" version="2.14"> <install version="1.0"> <actions> <action type="set_environment_for_install"> <repository changeset_revision="4c934f6b342e" name="package_r303" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/"> <package name="r303" version="3.0.3" /> </repository> </action> <action type="make_directory">$INSTALL_DIR</action> <action type="shell_command">export PATH=$PATH && R CMD BATCH $REPOSITORY_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 If atlas will not compile - eg: it thinks autoscaling is on or something, you need (eg for ubuntu) libopenblas-base installed on all nodes after commenting or removing all atlas references </readme> </package> </tool_dependency>