Mercurial > repos > mvdbeek > package_biocbasics_2_14

diff tool_dependencies.xml @ 0:f0ef1a7b157e draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/packages/package_ged_velvet commit 6e8989aa8aceed7487747212b2bb782755ed6cf5
author mvdbeek
date Tue, 20 Oct 2015 13:29:08 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Oct 20 13:29:08 2015 -0400
@@ -0,0 +1,87 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="R" version="3.1.2">
+        <repository changeset_revision="9f2fddb9d6e2" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="biocbasics" version="2.14">
+        <install version="1.0">
+            <actions>
+                <action type="setup_r_environment">
+                    <repository changeset_revision="9f2fddb9d6e2" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="R" version="3.1.2" />
+                    </repository>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/RColorBrewer_1.1-2.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/stringr_0.6.2.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/gtools_3.4.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/gdata_2.13.3.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/bitops_1.0-6.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/caTools_1.17.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/KernSmooth_2.23-13.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/gplots_2.15.0.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/limma_3.22.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/edgeR_3.8.5.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/BiocGenerics_0.12.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/S4Vectors_0.4.0.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/IRanges_2.0.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/GenomeInfoDb_1.2.4.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/XVector_0.6.0.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/GenomicRanges_1.18.3.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/Rcpp_0.11.3.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/RcppArmadillo_0.4.600.0.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/Biobase_2.26.0.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/codetools_0.2-9.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/iterators_1.0.7.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/foreach_1.4.2.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/checkmate_1.5.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/BBmisc_1.8.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/brew_1.0-6.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/DBI_0.3.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/digest_0.6.8.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/fail_1.2.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/RSQLite_1.0.0.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/base64enc_0.1-2.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/sendmailR_1.2-1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/BatchJobs_1.5.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/BiocParallel_1.0.0.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/AnnotationDbi_1.28.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/XML_3.98-1.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/xtable_1.7-4.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/annotate_1.44.0.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/survival_2.37-7.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/genefilter_1.48.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/lattice_0.20-29.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/latticeExtra_0.6-26.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/locfit_1.5-9.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/geneplotter_1.44.0.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/plyr_1.8.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/gtable_0.1.2.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/reshape2_1.4.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/dichromat_2.0-0.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/colorspace_1.2-4.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/munsell_0.4.2.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/labeling_0.3.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/scales_0.2.4.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/proto_0.3-10.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/MASS_7.3-35.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/ggplot2_1.0.0.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/Formula_1.1-2.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/cluster_1.15.3.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/rpart_4.1-8.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/nnet_7.3-8.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/acepack_1.3-3.3.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/foreign_0.8-61.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/Hmisc_3.14-6.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/DESeq2_1.6.3.tar.gz?raw=true</package>
+                    <package>https://bitbucket.org/mvdbeek/galaxy_downloads/downloads/DESeq_1.20.0.tar.gz</package>
+                    <package>https://bitbucket.org/mvdbeek/galaxy_downloads/downloads/gridExtra_0.9.1.tar.gz</package>
+                    <package>https://bitbucket.org/mvdbeek/galaxy_downloads/downloads/qvalue_1.43.0.tar.gz</package>
+                </action>
+            </actions>
+        </install>
+        <readme>
+        Differential gene expression analysis
+        You may need libxml2-dev for XML to compile
+        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
+        </readme>
+    </package>
+</tool_dependency>