Mercurial > repos > fubar > differential_count_models

annotate tool_dependencies.xml @ 108:96ebf676f6c0 draft

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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
author fubar
date Sun, 06 Jul 2014 02:36:47 -0400
parents
children 86bd60bea4d8
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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
fubar
parents:
diff changeset
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
fubar
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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
fubar
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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
fubar
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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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diff changeset
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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diff changeset
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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diff changeset
8 </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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diff changeset
9 <package name="r303" version="3.0.3">
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
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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diff changeset
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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diff changeset
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
parents:
diff changeset
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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diff changeset
16 <repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" 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
parents:
diff changeset
17 <package name="r303" version="3.0.3" />
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
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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diff changeset
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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diff changeset
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
fubar
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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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diff changeset
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
parents:
diff changeset
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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diff changeset
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
parents:
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
parents:
diff changeset
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>
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
27 <action type="shell_command">echo "quit(save=\"no\")" &gt;&gt; $INSTALL_DIR/runme.R</action>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
28 <action type="shell_command">echo "PATH=$PATH 1&gt;&amp;2"</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
parents:
diff changeset
29 <action type="shell_command">echo "R_PATH=$R_PATH 1&gt;&amp;2"</action>
96ebf676f6c0 consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
fubar
parents:
diff changeset
30 <action type="shell_command">export PATH=$PATH &amp;&amp; $R_PATH/R CMD BATCH $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
parents:
diff changeset
31 </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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diff changeset
32 </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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diff changeset
33 <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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34 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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35 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
parents:
diff changeset
36 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
37 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
38 </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
parents:
diff changeset
39 </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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40 </tool_dependency>