Mercurial > repos > fubar > differential_count_models

diff tool_dependencies.xml @ 132:0de946608423 draft

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author fubar
date Tue, 06 Jan 2015 02:20:55 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Jan 06 02:20:55 2015 -0500
@@ -0,0 +1,62 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="R" version="3.1.2">
+        <repository changeset_revision="f0626dac6765" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="graphicsmagick" version="1.3.18">
+        <repository changeset_revision="bff3f66adff2" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="ghostscript" version="9.10">
+        <repository changeset_revision="9345d2740f0c" name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+
+    <package name="biocbasics" version="2.14">
+        <install version="1.0">
+            <actions>
+                <action type="setup_r_environment">
+                    <repository changeset_revision="f0626dac6765" name="package_r_3_1_2" owner="iuc" toolshed="https://testtoolshed.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/survival_2.37-7.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/lars_1.2.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/lattice_0.20-29.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/latticeExtra_0.6-26.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/Matrix_1.1-4.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/glmnet_1.9-8.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/KernSmooth_2.23-13.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/numDeriv_2012.9-1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/lava_1.3.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/prodlim_1.5.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/codetools_0.2-9.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/iterators_1.0.7.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/foreach_1.4.2.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/Formula_1.1-2.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/RColorBrewer_1.1-2.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/cluster_1.15.3.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rpart_4.1-8.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/nnet_7.3-8.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/acepack_1.3-3.3.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/foreign_0.8-61.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/Hmisc_3.14-6.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/SparseM_1.05.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/quantreg_5.05.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/nlme_3.1-118.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/polspline_1.1.9.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/mvtnorm_1.0-2.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/TH.data_1.0-5.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/zoo_1.7-11.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/sandwich_2.3-2.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/multcomp_1.3-8.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rms_4.2-1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/pec_2.4.4.tar.gz?raw=true</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>