comparison tool_dependencies.xml @ 38:2f7573aacac3 draft

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author fubar
date Sun, 22 Dec 2013 02:57:05 -0500
parents b8f9b2c64202
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37:9cec7795c52f 38:2f7573aacac3
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="r3" version="3.0.1">
4 <repository changeset_revision="6e89ec508745" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
5 </package>
6 <package name="ghostscript" version="9.07">
7 <repository changeset_revision="7245d8573fca" name="package_ghostscript_9_07" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
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="2.12">
13 <install version="1.0">
14 <actions>
15 <action type="set_environment_for_install">
16 <repository changeset_revision="6e89ec508745" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/">
17 <package name="r3" version="3.0.1" />
18 </repository>
19 </action>
20 <action type="make_directory">$INSTALL_DIR</action>
21 <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" &gt; $INSTALL_DIR/runme.R</action>
22 <action type="shell_command">echo "installme=c('edgeR','limma','DESeq','DESeq2')" &gt;&gt; $INSTALL_DIR/runme.R</action>
23 <action type="shell_command">echo "biocLite()" &gt;&gt; $INSTALL_DIR/runme.R</action>
24 <action type="shell_command">echo "biocLite(installme)" &gt;&gt; $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')" &gt;&gt; $INSTALL_DIR/runme.R</action>
26 <action type="shell_command">echo "quit(save='no')" &gt;&gt; $INSTALL_DIR/runme.R</action>
27 <action type="shell_command"> export PATH=$PATH &amp;&amp; export R_HOME=$R_HOME &amp;&amp; export R_LIBS=$R_LIBS &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R </action>
28 </actions>
29 </install>
30 <readme>Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick
31 (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 copyright ross lazarus last updated december 2013 ross stop lazarus at gmail stop com
35 License to use this source (dependencies have their own obligations)
36 is made available to you under the terms of the LGPL
37 </readme>
38 </package>
39 </tool_dependency>