| Previous changeset 95:8c96a2d95436 (2014-03-02) Next changeset 97:395197c30bf7 (2014-03-02) |
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Commit message:
Uploaded |
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modified:
tool_dependencies.xml |
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| diff -r 8c96a2d95436 -r e7d02e6b253c tool_dependencies.xml --- a/tool_dependencies.xml Sun Mar 02 22:35:18 2014 -0500 +++ b/tool_dependencies.xml Sun Mar 02 23:01:19 2014 -0500 |
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| @@ -9,6 +9,9 @@ <package name="r303" version="3.0.3"> <repository changeset_revision="4c934f6b342e" name="package_r303" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> </package> + <set_environment version="1.0"> + <environment_variable action="set_to" name="RUNME_PATH">$REPOSITORY_INSTALL_DIR</environment_variable> + </set_environment> <package name="biocbasics" version="2.14"> <install version="1.0"> <actions> @@ -18,9 +21,8 @@ </repository> </action> <action type="make_directory">$INSTALL_DIR</action> - <action type="shell_command">echo `ls -l`</action> - - <action type="shell_command">export PATH=$PATH && R CMD BATCH ./runme.R </action> + <action type="shell_command">ls -l</action> + <action type="shell_command">export PATH=$PATH && R CMD BATCH $RUNME_PATH/runme.R </action> </actions> </install> <readme>Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick (replaces imagemagick) and ghostscript for compressing R's bloated pdfs |