| Previous changeset 69:919822102c86 (2014-02-17) Next changeset 71:f33aac17f15d (2014-02-18) |
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Commit message:
Uploaded |
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modified:
tool_dependencies.xml |
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| diff -r 919822102c86 -r e4291e5a03c1 tool_dependencies.xml --- a/tool_dependencies.xml Mon Feb 17 18:46:46 2014 -0500 +++ b/tool_dependencies.xml Tue Feb 18 01:07:24 2014 -0500 |
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| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tool_dependency> <package name="r302" version="3.0.2"> - <repository changeset_revision="ce4a3c48dbd7" name="package_r302" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + <repository changeset_revision="c161b72d384e" name="package_r302" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> </package> <package name="ghostscript" version="9.10"> <repository changeset_revision="9345d2740f0c" name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> @@ -13,7 +13,7 @@ <install version="1.0"> <actions> <action type="set_environment_for_install"> - <repository changeset_revision="ce4a3c48dbd7" name="package_r302" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/"> + <repository changeset_revision="c161b72d384e" name="package_r302" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/"> <package name="r302" version="3.0.2" /> </repository> </action> @@ -24,7 +24,8 @@ <action type="shell_command">echo "biocLite(installme)" >> $INSTALL_DIR/runme.R</action> <action type="shell_command">echo "install.packages(c('stringr','gplots'),dependencies=T,repos='http://cran.us.r-project.org')" >> $INSTALL_DIR/runme.R</action> <action type="shell_command">echo "quit(save='no')" >> $INSTALL_DIR/runme.R</action> - <action type="shell_command"> export PATH=$PATH && export R_HOME=$R_HOME && export R_LIBS=$R_LIBS && $R_PATH/R CMD BATCH $INSTALL_DIR/runme.R </action> + <action type="shell_command" /> + <action type="shell_command"> export PATH=$PATH && echo "PATH=$PATH" && export R_HOME=$R_HOME && export R_LIBS=$R_LIBS && R CMD BATCH $INSTALL_DIR/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 |