Mercurial > repos > fubar > differential_count_models
annotate tool_dependencies.xml @ 110:d7e2a0c0cce9 draft
Uploaded
author | fubar |
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date | Sun, 06 Jul 2014 21:00:54 -0400 |
parents | 86bd60bea4d8 |
children | 9f2e0ec3e826 |
rev | line source |
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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:
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changeset
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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
fubar
parents:
diff
changeset
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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
parents:
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changeset
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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
parents:
diff
changeset
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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
parents:
diff
changeset
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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
parents:
diff
changeset
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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
parents:
diff
changeset
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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
parents:
diff
changeset
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8 </package> |
110 | 9 <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
parents:
diff
changeset
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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
parents:
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
parents:
diff
changeset
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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
parents:
diff
changeset
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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
parents:
diff
changeset
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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
parents:
diff
changeset
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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
parents:
diff
changeset
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16 <repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> |
110 | 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
parents:
diff
changeset
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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
parents:
diff
changeset
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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
parents:
diff
changeset
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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
fubar
parents:
diff
changeset
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21 <action type="shell_command">echo "bioclite=\"http://bioconductor.org/biocLite.R\"" > $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
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22 <action type="shell_command">echo "source(bioclite)" >> $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
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23 <action type="shell_command">echo "installme=c(\"edgeR\",\"limma\",\"DESeq\",\"DESeq2\")" >> $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
|
24 <action type="shell_command">echo "biocLite()" >> $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)" >> $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\")" >> $INSTALL_DIR/runme.R</action> |
109 | 27 <action type="shell_command">echo "quit(save=\"no\")" >> $INSTALL_DIR/runme.R</action> |
28 <action type="shell_command">export PATH=$PATH && R CMD BATCH $INSTALL_DIR/runme.R </action> | |
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
|
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
parents:
diff
changeset
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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
fubar
parents:
diff
changeset
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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
parents:
diff
changeset
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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
parents:
diff
changeset
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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
parents:
diff
changeset
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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
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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
parents:
diff
changeset
|
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
fubar
parents:
diff
changeset
|
38 </tool_dependency> |