Mercurial > repos > fubar > differential_count_models

annotate tool_dependencies.xml @ 130:a9ffdf5f7d2a draft

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with tests
author fubar
date Thu, 01 Jan 2015 21:53:07 -0500
parents a95f5496d330
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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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
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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>
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3 <package name="R_3_1_1" version="3.1.1">
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4 <repository changeset_revision="63cdb9b2234c" name="package_r_3_1_1" owner="fubar" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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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
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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="bff3f66adff2" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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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
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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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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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11 </package>
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12
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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
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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="63cdb9b2234c" 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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22 <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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23 <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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25 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/stringr_0.6.2.tar.gz?raw=true</package>
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26 <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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28 <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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29 <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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30 <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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31 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/GenomeInfoDb_1.0.2.tar.gz?raw=true</package>
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33 <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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34 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/XVector_0.4.0.tar.gz?raw=true</package>
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35 <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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36 <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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37 <!--
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38 <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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39 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/digest_0.6.4.tar.gz?raw=true</package>
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40 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/labeling_0.3.tar.gz?raw=true</package>
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41 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/colorspace_1.2-4.tar.gz?raw=true</package>
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42 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/munsell_0.4.2.tar.gz?raw=true</package>
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43 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/dichromat_2.0-0.tar.gz?raw=true</package>
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44 <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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45 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/scales_0.2.4.tar.gz?raw=true</package>
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46 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/gtable_0.1.2.tar.gz?raw=true</package>
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47 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/plyr_1.8.1.tar.gz?raw=true</package>
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48 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/statmod_1.4.20.tar.gz?raw=true</package>
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49 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/proto_0.3-10.tar.gz?raw=true</package>
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50 <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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51 -->
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52 <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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53 <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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54 <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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56 <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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57 <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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58 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/geneplotter_1.42.0.tar.gz?raw=true</package>
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59 <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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60 <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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62 <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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63 <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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64 <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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65 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/bitops_1.0-6.tar.gz?raw=true</package>
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66 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/gtools_3.4.1.tar.gz?raw=true</package>
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67 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/gdata_2.13.3.tar.gz?raw=true</package>
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68 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/caTools_1.17.1.tar.gz?raw=true</package>
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69 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/gplots_2.14.2.tar.gz?raw=true</package>
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70 </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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71 </actions>
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72 </install>
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73 <readme>
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74 Differential gene expression analysis
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75 You may need libxml2-dev for XML to compile
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76 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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77 </readme>
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78 </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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79 </tool_dependency>