Mercurial > repos > fubar > differential_count_models

annotate tool_dependencies.xml @ 113:dd8cbcb35518 draft

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author fubar
date Wed, 22 Oct 2014 23:48:07 -0400
parents 525f2edd36d7
children 616c780f69a6
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="R_3_1_1" version="3.1.1">
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4 <repository changeset_revision="6ca21e466ef6" name="package_r_3_1_1" owner="fubar" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="graphicsmagick" version="1.3.18">
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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" />
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8 </package>
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9 <package name="ghostscript" version="9.10">
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10 <repository changeset_revision="9345d2740f0c" name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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11 </package>
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12
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13 <package name="biocbasics" version="2.14">
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14 <install version="1.0">
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15 <actions>
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16 <action type="setup_r_environment">
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17 <repository changeset_revision="6ca21e466ef6" name="package_r_3_1_1" owner="fubar" toolshed="https://testtoolshed.g2.bx.psu.edu">
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18 <package name="R_3_1_1" version="3.1.1" />
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19 </repository>
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20 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/RSQLite_0.11.4.tar.gz?raw=true</package>
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21 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/Biobase_2.24.0.tar.gz?raw=true</package>
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22 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/BiocGenerics_0.10.0.tar.gz?raw=true</package>
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23 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/DBI_0.3.1.tar.gz?raw=true</package>
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24 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/GenomicRanges_1.16.4.tar.gz?raw=true</package>
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25 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/IRanges_1.22.10.tar.gz?raw=true</package>
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26 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/RColorBrewer_1.0-5.tar.gz?raw=true</package>
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27 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/RcppArmadillo_0.4.450.1.0.tar.gz?raw=true</package>
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28 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/Rcpp_0.11.3.tar.gz?raw=true</package>
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29 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/XML_3.98-1.1.tar.gz?raw=true</package>
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30 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/annotate_1.42.1.tar.gz?raw=true</package>
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31 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/locfit_1.5-9.1.tar.gz?raw=true</package>
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32 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/reshape2_1.4.tar.gz?raw=true</package>
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33 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rjson_0.2.14.tar.gz?raw=true</package>
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34 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/xtable_1.7-4.tar.gz?raw=true</package>
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35 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/AnnotationDbi_1.26.1.tar.gz?raw=true</package>
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36 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/DESeq2_1.4.5.tar.gz?raw=true</package>
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37 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/edgeR_3.6.8.tar.gz?raw=true</package>
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38 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/genefilter_1.46.1.tar.gz?raw=true</package>
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39 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/getopt_1.20.0.tar.gz?raw=true</package>
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40 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/ggplot2_1.0.0.tar.gz?raw=true</package>
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41 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/limma_3.20.9.tar.gz?raw=true</package>
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42 </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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43 </actions>
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44 </install>
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45 <readme>
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46 Differential gene expression analysis
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47 Ubuntu has a bug with libgfortran. To fix that create a symlink like: sudo ln -s /usr/lib/x86_64-linux-gnu/libgfortran.so.3 /usr/lib/x86_64-linux-gnu/libgfortran.so
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48 </readme>
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49 </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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50 </tool_dependency>