Mercurial > repos > fubar > differential_count_models

annotate tool_dependencies.xml @ 110:d7e2a0c0cce9 draft

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author fubar
date Sun, 06 Jul 2014 21:00:54 -0400
parents 86bd60bea4d8
children 9f2e0ec3e826
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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108
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
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1 <?xml version="1.0"?>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
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2 <tool_dependency>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
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3 <package name="ghostscript" version="9.10">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
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4 <repository changeset_revision="9345d2740f0c" name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
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5 </package>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
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6 <package name="graphicsmagick" version="1.3.18">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
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7 <repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
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8 </package>
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d7e2a0c0cce9 Uploaded
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9 <package name="R" version="3.0.3">
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96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
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10 <repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
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11 </package>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
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12 <package name="biocbasics" version="2.14">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
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13 <install version="1.0">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
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14 <actions>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
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15 <action type="set_environment_for_install">
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
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16 <repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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d7e2a0c0cce9 Uploaded
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diff changeset
17 <package name="R" version="3.0.3" />
108
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
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18 </repository>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
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19 </action>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
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20 <action type="make_directory">$INSTALL_DIR</action>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
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21 <action type="shell_command">echo "bioclite=\"http://bioconductor.org/biocLite.R\"" &gt; $INSTALL_DIR/runme.R</action>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
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22 <action type="shell_command">echo "source(bioclite)" &gt;&gt; $INSTALL_DIR/runme.R</action>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
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23 <action type="shell_command">echo "installme=c(\"edgeR\",\"limma\",\"DESeq\",\"DESeq2\")" &gt;&gt; $INSTALL_DIR/runme.R</action>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
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24 <action type="shell_command">echo "biocLite()" &gt;&gt; $INSTALL_DIR/runme.R</action>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
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diff changeset
25 <action type="shell_command">echo "biocLite(installme)" &gt;&gt; $INSTALL_DIR/runme.R</action>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
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26 <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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27 <action type="shell_command">echo "quit(save=\"no\")" &gt;&gt; $INSTALL_DIR/runme.R</action>
86bd60bea4d8 Uploaded
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28 <action type="shell_command">export PATH=$PATH &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R </action>
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96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
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diff changeset
29 </actions>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
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30 </install>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
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31 <readme>Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick (replaces imagemagick) and ghostscript for compressing R's bloated pdfs
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
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32 It's clunky but this is the most convenient way I could get anything installed into the package_r3
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
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33 Note we use cran at fred hutch since no fastest mirror thingy
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
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34 If atlas will not compile - eg: it thinks autoscaling is on or something,
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
35 you need (eg for ubuntu) libopenblas-base installed on all nodes after commenting or removing all atlas references
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
36 </readme>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
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37 </package>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
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38 </tool_dependency>