Mercurial > repos > bgruening > package_rpy2_2_3_6

changeset 1:dd4ad562094e draft

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Uploaded
author bgruening
date Sun, 30 Jun 2013 18:06:31 -0400
parents 67c8b836d765
children 4bc1c94efdff
files tool_dependencies.xml
diffstat 1 files changed, 9 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Sun Jun 30 17:00:34 2013 -0400
+++ b/tool_dependencies.xml	Sun Jun 30 18:06:31 2013 -0400
@@ -1,31 +1,29 @@
 <?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" />
+        <repository changeset_revision="856591655486" name="precommit_test" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
 
-
-
-    <package name="deseq2" version="1.0.17">
+    <package name="rpy2_2_3_6" version="2.3.6">
         <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="download_by_url">https://pypi.python.org/packages/source/r/rpy2/rpy2-2.3.6.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">
+                    <repository changeset_revision="856591655486" 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>
+                export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
+                python setup.py install --home $INSTALL_DIR --r-home $R_HOME</action>
+
                 <action type="set_environment">
-                    <environment_variable action="append_to" name="R_LIBS">$INSTALL_DIR/deseq2/</environment_variable>
+                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
                 </action>
             </actions>
         </install>
-        <readme>DESeq2</readme>
+        <readme />
     </package>
 </tool_dependency>