Mercurial > repos > fubar > differential_count_models
diff tool_dependencies.xml @ 108:96ebf676f6c0 draft
consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful
| author | fubar |
|---|---|
| date | Sun, 06 Jul 2014 02:36:47 -0400 |
| parents | |
| children | 86bd60bea4d8 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sun Jul 06 02:36:47 2014 -0400 @@ -0,0 +1,40 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="ghostscript" version="9.10"> + <repository changeset_revision="9345d2740f0c" name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="graphicsmagick" version="1.3.18"> + <repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="r303" version="3.0.3"> + <repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="biocbasics" version="2.14"> + <install version="1.0"> + <actions> + <action type="set_environment_for_install"> + <repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="r303" version="3.0.3" /> + </repository> + </action> + <action type="make_directory">$INSTALL_DIR</action> + <action type="shell_command">echo "bioclite=\"http://bioconductor.org/biocLite.R\"" > $INSTALL_DIR/runme.R</action> + <action type="shell_command">echo "source(bioclite)" >> $INSTALL_DIR/runme.R</action> + <action type="shell_command">echo "installme=c(\"edgeR\",\"limma\",\"DESeq\",\"DESeq2\")" >> $INSTALL_DIR/runme.R</action> + <action type="shell_command">echo "biocLite()" >> $INSTALL_DIR/runme.R</action> + <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\")" >> $INSTALL_DIR/runme.R</action> + <action type="shell_command">echo "PATH=$PATH 1>&2"</action> + <action type="shell_command">echo "R_PATH=$R_PATH 1>&2"</action> + <action type="shell_command">export PATH=$PATH && $R_PATH/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 + It's clunky but this is the most convenient way I could get anything installed into the package_r3 + Note we use cran at fred hutch since no fastest mirror thingy + If atlas will not compile - eg: it thinks autoscaling is on or something, + you need (eg for ubuntu) libopenblas-base installed on all nodes after commenting or removing all atlas references + </readme> + </package> +</tool_dependency>