Mercurial > repos > bgruening > package_rpy2_2_3_6

changeset 0:67c8b836d765 draft

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Uploaded
author bgruening
date Sun, 30 Jun 2013 17:00:34 -0400
parents
children dd4ad562094e
files tool_dependencies.xml
diffstat 1 files changed, 31 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Sun Jun 30 17:00:34 2013 -0400
@@ -0,0 +1,31 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="R_3_0_1" version="3.0.1">
+        <repository changeset_revision="4e9dce1105cd" 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="download_file">http://bioconductor.org/packages/release/bioc/src/contrib/DESeq2_1.0.17.tar.gz</action>
+
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="4e9dce1105cd" 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">$INSTALL_DIR/deseq2/</action>
+                <action type="shell_command">
+                    Rscript -e "source('http://bioconductor.org/biocLite.R'); install.packages('DESeq2', lib='$INSTALL_DIR/deseq2/', repos='http://cran.us.r-project.org')"
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="append_to" name="R_LIBS">$INSTALL_DIR/deseq2/</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>DESeq2</readme>
+    </package>
+</tool_dependency>