Mercurial > repos > fubar > differential_count_models

annotate tool_dependencies.xml @ 48:1c6c7e481be7 draft

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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
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48
1c6c7e481be7 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
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1 <?xml version="1.0"?>
1c6c7e481be7 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
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2 <tool_dependency>
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3 <!--
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4 this will not compile for me - it thinks we have autoscaling on
1c6c7e481be7 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
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5 - so we need libopenblas-base installed on all nodes...grrr
1c6c7e481be7 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
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6 <package name="atlas" version="3.11.11">
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7 <repository name='package_atlas_3_11' owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
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8 </package>
1c6c7e481be7 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
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9 and we need this added to the set_environment section below too
1c6c7e481be7 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
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10 <repository name="package_atlas_3_11" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
1c6c7e481be7 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
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11 <package name="atlas" version="3.11.11" />
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12 </repository>
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13 -->
1c6c7e481be7 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
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14 <package name="r3" version="3.0.1">
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15 <repository changeset_revision="6e89ec508745" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
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16 </package>
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17 <package name="ghostscript" version="9.07">
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18 <repository changeset_revision="7245d8573fca" name="package_ghostscript_9_07" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
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19 </package>
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20 <package name="graphicsmagick" version="1.3.18">
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21 <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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22 </package>
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23 <package name="biocbasics" version="2.12">
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24 <install version="1.0">
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25 <actions>
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26 <action type="set_environment_for_install">
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27 <repository changeset_revision="6e89ec508745" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/">
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28 <package name="r3" version="3.0.1" />
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29 </repository>
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30 </action>
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31 <action type="make_directory">$INSTALL_DIR</action>
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32 <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" &gt; $INSTALL_DIR/runme.R</action>
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33 <action type="shell_command">echo "installme=c('edgeR','limma','DESeq','DESeq2')" &gt;&gt; $INSTALL_DIR/runme.R</action>
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34 <action type="shell_command">echo "biocLite()" &gt;&gt; $INSTALL_DIR/runme.R</action>
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35 <action type="shell_command">echo "biocLite(installme)" &gt;&gt; $INSTALL_DIR/runme.R</action>
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36 <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>
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37 <action type="shell_command">echo "quit(save='no')" &gt;&gt; $INSTALL_DIR/runme.R</action>
1c6c7e481be7 removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.
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38 <action type="shell_command"> export PATH=$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>
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39 </actions>
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40 </install>
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41 <readme>Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick
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42 (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 copyright ross lazarus last updated december 2013 ross stop lazarus at gmail stop com
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46 License to use this source (dependencies have their own obligations)
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47 is made available to you under the terms of the LGPL
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48 </readme>
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49 </package>
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50 </tool_dependency>