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61
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <!--
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4 Atlas will not compile for me - it thinks we have autoscaling on
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5 so we need libopenblas-base installed on all nodes after commenting this and the set environment reference...
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6 grrr
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7 -->
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8 <package name="atlas" version="3.11.11">
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9 <repository changeset_revision="02bc9f241131" name="package_atlas_3_11" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
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10 </package>
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11
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12 <package name="r302" version="3.0.2">
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13 <repository changeset_revision="e5d9e2ca3ba6" name="package_r302" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
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14 </package>
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15 <package name="ghostscript" version="9.10">
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16 <repository changeset_revision="9345d2740f0c" name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
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17 </package>
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18 <package name="graphicsmagick" version="1.3.18">
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19 <repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
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20 </package>
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21 <package name="biocbasics" version="2.14">
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22 <install version="1.0">
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23 <actions>
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24 <action type="set_environment_for_install">
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25 <repository changeset_revision="e5d9e2ca3ba6" name="package_r302" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/">
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26 <package name="r302" version="3.0.2" />
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27 </repository>
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28 <repository changeset_revision="02bc9f241131" name="package_atlas_3_11" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
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29 <package name="atlas" version="3.11.11" />
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30 </repository>
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31 </action>
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32 <action type="make_directory">$INSTALL_DIR</action>
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33 <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" > $INSTALL_DIR/runme.R</action>
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34 <action type="shell_command">echo "installme=c('edgeR','limma','DESeq','DESeq2')" >> $INSTALL_DIR/runme.R</action>
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35 <action type="shell_command">echo "biocLite()" >> $INSTALL_DIR/runme.R</action>
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36 <action type="shell_command">echo "biocLite(installme)" >> $INSTALL_DIR/runme.R</action>
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37 <action type="shell_command">echo "install.packages(c('stringr','gplots'),dependencies=T,repos='http://cran.us.r-project.org')" >> $INSTALL_DIR/runme.R</action>
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38 <action type="shell_command">echo "quit(save='no')" >> $INSTALL_DIR/runme.R</action>
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39 <action type="shell_command"> export PATH=$PATH && export R_HOME=$R_HOME && export R_LIBS=$R_LIBS && R CMD BATCH $INSTALL_DIR/runme.R </action>
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40 </actions>
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41 </install>
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42 <readme>Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick (replaces imagemagick) and ghostscript for compressing R's bloated pdfs
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43 It's clunky but this is the most convenient way I could get anything installed into the package_r3
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44 Note we use cran at fred hutch since no fastest mirror thingy
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45 If atlas will not compile - eg: it thinks autoscaling is on or something,
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46 you need (eg for ubuntu) libopenblas-base installed on all nodes after commenting or removing all atlas references
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47 </readme>
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48 </package>
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49 </tool_dependency>
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