changeset 0:912bdcdc5949 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Jul 01 06:24:33 2013 -0400
@@ -0,0 +1,33 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="R_3_0_1" version="3.0.1">
+        <repository changeset_revision="564b46e4fda7" name="precommit_test" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+
+    <package name="deseq2" version="1.0.17">
+        <install version="1.0">
+            <actions>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="564b46e4fda7" name="precommit_test" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="R_3_0_1" version="3.0.1" />
+                    </repository>
+                </action>
+
+                <action type="make_directory">$INSTALL_DIR/deseq2/</action>
+                <action type="shell_command">
+                    export PATH=$PATH:$R_HOME/bin &amp;&amp; 
+                    export R_LIBS=$INSTALL_DIR/deseq2/ &amp;&amp; 
+                    Rscript -e "source('http://bioconductor.org/biocLite.R'); biocLite('DESeq2')"
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="append_to" name="R_LIBS">$INSTALL_DIR/deseq2/</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+        Differential gene expression analysis based on the negative binomial distribution.
+        http://www.bioconductor.org/packages/2.12/bioc/html/DESeq2.html
+        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>