Mercurial > repos > fubar > differential_count_models
comparison tool_dependencies.xml @ 136:635f944c2499 draft
Uploaded
| author | fubar |
|---|---|
| date | Tue, 06 Jan 2015 19:36:41 -0500 |
| parents | |
| children | 48a6a92bbc30 |
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| 135:543556234f0c | 136:635f944c2499 |
|---|---|
| 1 <?xml version="1.0"?> | |
| 2 <tool_dependency> | |
| 3 <package name="R" version="3.1.2"> | |
| 4 <repository changeset_revision="f0626dac6765" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> | |
| 5 </package> | |
| 6 <package name="graphicsmagick" version="1.3.18"> | |
| 7 <repository changeset_revision="bff3f66adff2" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> | |
| 8 </package> | |
| 9 <package name="ghostscript" version="9.10"> | |
| 10 <repository changeset_revision="9345d2740f0c" name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> | |
| 11 </package> | |
| 12 | |
| 13 <package name="biocbasics" version="2.14"> | |
| 14 <install version="1.0"> | |
| 15 <actions> | |
| 16 <action type="setup_r_environment"> | |
| 17 <repository changeset_revision="f0626dac6765" name="package_r_3_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> | |
| 18 <package name="R" version="3.1.2" /> | |
| 19 </repository> | |
| 20 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/stringr_0.6.2.tar.gz?raw=true</package> | |
| 21 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/gtools_3.4.1.tar.gz?raw=true</package> | |
| 22 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/gdata_2.13.3.tar.gz?raw=true</package> | |
| 23 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/bitops_1.0-6.tar.gz?raw=true</package> | |
| 24 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/caTools_1.17.1.tar.gz?raw=true</package> | |
| 25 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/KernSmooth_2.23-13.tar.gz?raw=true</package> | |
| 26 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/gplots_2.15.0.tar.gz?raw=true</package> | |
| 27 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/limma_3.22.1.tar.gz?raw=true</package> | |
| 28 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/edgeR_3.8.5.tar.gz?raw=true</package> | |
| 29 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/BiocGenerics_0.8.0.tar.gz?raw=true</package> | |
| 30 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/S4Vectors_0.4.0.tar.gz?raw=true</package> | |
| 31 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/IRanges_2.0.1.tar.gz?raw=true</package> | |
| 32 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/GenomeInfoDb_1.2.4.tar.gz?raw=true</package> | |
| 33 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/XVector_0.6.0.tar.gz?raw=true</package> | |
| 34 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/GenomicRanges_1.18.3.tar.gz?raw=true</package> | |
| 35 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/RcppArmadillo_0.4.600.0.tar.gz?raw=true</package> | |
| 36 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/Biobase_2.26.0.tar.gz?raw=true</package> | |
| 37 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/codetools_0.2-9.tar.gz?raw=true</package> | |
| 38 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/iterators_1.0.7.tar.gz?raw=true</package> | |
| 39 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/foreach_1.4.2.tar.gz?raw=true</package> | |
| 40 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/checkmate_1.5.1.tar.gz?raw=true</package> | |
| 41 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/BBmisc_1.8.tar.gz?raw=true</package> | |
| 42 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/brew_1.0-6.tar.gz?raw=true</package> | |
| 43 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/DBI_0.3.1.tar.gz?raw=true</package> | |
| 44 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/digest_0.6.8.tar.gz?raw=true</package> | |
| 45 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/fail_1.2.tar.gz?raw=true</package> | |
| 46 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/RSQLite_1.0.0.tar.gz?raw=true</package> | |
| 47 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/base64enc_0.1-2.tar.gz?raw=true</package> | |
| 48 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/sendmailR_1.2-1.tar.gz?raw=true</package> | |
| 49 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/BatchJobs_1.5.tar.gz?raw=true</package> | |
| 50 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/BiocParallel_1.0.0.tar.gz?raw=true</package> | |
| 51 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/AnnotationDbi_1.28.1.tar.gz?raw=true</package> | |
| 52 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/XML_3.98-1.1.tar.gz?raw=true</package> | |
| 53 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/xtable_1.7-4.tar.gz?raw=true</package> | |
| 54 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/annotate_1.44.0.tar.gz?raw=true</package> | |
| 55 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/survival_2.37-7.tar.gz?raw=true</package> | |
| 56 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/genefilter_1.48.1.tar.gz?raw=true</package> | |
| 57 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/latticeExtra_0.6-26.tar.gz?raw=true</package> | |
| 58 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/locfit_1.5-9.1.tar.gz?raw=true</package> | |
| 59 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/RColorBrewer_1.1-2.tar.gz?raw=true</package> | |
| 60 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/geneplotter_1.44.0.tar.gz?raw=true</package> | |
| 61 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/plyr_1.8.1.tar.gz?raw=true</package> | |
| 62 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/gtable_0.1.2.tar.gz?raw=true</package> | |
| 63 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/reshape2_1.4.tar.gz?raw=true</package> | |
| 64 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/dichromat_2.0-0.tar.gz?raw=true</package> | |
| 65 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/colorspace_1.2-4.tar.gz?raw=true</package> | |
| 66 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/munsell_0.4.2.tar.gz?raw=true</package> | |
| 67 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/labeling_0.3.tar.gz?raw=true</package> | |
| 68 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/scales_0.2.4.tar.gz?raw=true</package> | |
| 69 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/proto_0.3-10.tar.gz?raw=true</package> | |
| 70 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/MASS_7.3-35.tar.gz?raw=true</package> | |
| 71 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/ggplot2_1.0.0.tar.gz?raw=true</package> | |
| 72 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/Formula_1.1-2.tar.gz?raw=true</package> | |
| 73 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/cluster_1.15.3.tar.gz?raw=true</package> | |
| 74 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rpart_4.1-8.tar.gz?raw=true</package> | |
| 75 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/nnet_7.3-8.tar.gz?raw=true</package> | |
| 76 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/acepack_1.3-3.3.tar.gz?raw=true</package> | |
| 77 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/foreign_0.8-61.tar.gz?raw=true</package> | |
| 78 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/Hmisc_3.14-6.tar.gz?raw=true</package> | |
| 79 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/DESeq2_1.6.3.tar.gz?raw=true</package> | |
| 80 | |
| 81 </action> | |
| 82 </actions> | |
| 83 </install> | |
| 84 <readme> | |
| 85 Differential gene expression analysis | |
| 86 You may need libxml2-dev for XML to compile | |
| 87 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 | |
| 88 </readme> | |
| 89 </package> | |
| 90 </tool_dependency> |