| Previous changeset 36:46c91da1351e (2013-06-13) Next changeset 38:ba361e7ebc17 (2013-06-13) |
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rgedgeR/tool_dependencies.xml |
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| diff -r 46c91da1351e -r faf413433dca rgedgeR/tool_dependencies.xml --- a/rgedgeR/tool_dependencies.xml Thu Jun 13 00:01:11 2013 -0400 +++ b/rgedgeR/tool_dependencies.xml Thu Jun 13 00:34:29 2013 -0400 |
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| @@ -1,20 +1,17 @@ <?xml version="1.0"?> <tool_dependency> - <set_environment version="1.0"> - <environment_variable action="set_to" name="R_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable> - </set_environment> <package name="package_r3" version="3.0.1"> - <repository changeset_revision="addf8c9c778a" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + <repository changeset_revision="6344ee60d0cf" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> </package> <package name="biocbasics" version="2.12"> <install version="1.0"> <actions> <action type="set_environment_for_install"> - <repository changeset_revision="addf8c9c778a" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/"> + <repository changeset_revision="6344ee60d0cf" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/"> <package name="r3" version="3.0.1" /> </repository> </action> - <action type="shell_command">R CMD BATCH $R_SCRIPT_PATH/rgedgeR/installBioC.R </action> + <action type="shell_command">R CMD BATCH ${REPOSITORY_INSTALL_DIR}/rgedgeR/installBioC.R </action> </actions> </install> <readme>Installs some basic bioc packages for the edgeR tool |