61
+ − 1 <?xml version="1.0"?>
+ − 2 <tool_dependency>
84
+ − 3 <package name="r303" version="3.0.3">
+ − 4 <repository changeset_revision="113ad1e5336c" name="package_r303" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
76
+ − 5 </package>
+ − 6 <package name="ghostscript" version="9.07">
+ − 7 <repository changeset_revision="10222a7db54c" name="package_ghostscript_9_07" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
61
+ − 8 </package>
+ − 9 <package name="graphicsmagick" version="1.3.18">
+ − 10 <repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+ − 11 </package>
+ − 12 <package name="biocbasics" version="2.14">
+ − 13 <install version="1.0">
+ − 14 <actions>
+ − 15 <action type="set_environment_for_install">
75
+ − 16 <repository changeset_revision="c881f61d208e" name="package_r302" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/">
61
+ − 17 <package name="r302" version="3.0.2" />
+ − 18 </repository>
+ − 19 </action>
+ − 20 <action type="make_directory">$INSTALL_DIR</action>
+ − 21 <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" > $INSTALL_DIR/runme.R</action>
+ − 22 <action type="shell_command">echo "installme=c('edgeR','limma','DESeq','DESeq2')" >> $INSTALL_DIR/runme.R</action>
+ − 23 <action type="shell_command">echo "biocLite()" >> $INSTALL_DIR/runme.R</action>
+ − 24 <action type="shell_command">echo "biocLite(installme)" >> $INSTALL_DIR/runme.R</action>
+ − 25 <action type="shell_command">echo "install.packages(c('stringr','gplots'),dependencies=T,repos='http://cran.us.r-project.org')" >> $INSTALL_DIR/runme.R</action>
+ − 26 <action type="shell_command">echo "quit(save='no')" >> $INSTALL_DIR/runme.R</action>
76
+ − 27 <action type="shell_command">echo "PATH=$PATH 1>&2"</action>
+ − 28 <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>
61
+ − 29 </actions>
+ − 30 </install>
+ − 31 <readme>Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick (replaces imagemagick) and ghostscript for compressing R's bloated pdfs
+ − 32 It's clunky but this is the most convenient way I could get anything installed into the package_r3
+ − 33 Note we use cran at fred hutch since no fastest mirror thingy
+ − 34 If atlas will not compile - eg: it thinks autoscaling is on or something,
+ − 35 you need (eg for ubuntu) libopenblas-base installed on all nodes after commenting or removing all atlas references
+ − 36 </readme>
+ − 37 </package>
+ − 38 </tool_dependency>