Mercurial > repos > fubar > differential_count_models
comparison tool_dependencies.xml @ 91:6fb919a3bff4 draft
Uploaded
| author | fubar |
|---|---|
| date | Sun, 02 Mar 2014 19:49:16 -0500 |
| parents | 2c7b33c84904 |
| children | 34ef458b7fd9 |
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| 90:2c7b33c84904 | 91:6fb919a3bff4 |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | 2 <tool_dependency> |
| 3 <package name="r303" version="3.0.3"> | |
| 4 <repository changeset_revision="826f08ed8859" name="package_r303" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> | |
| 5 </package> | |
| 6 <package name="ghostscript" version="9.07"> | 3 <package name="ghostscript" version="9.07"> |
| 7 <repository changeset_revision="10222a7db54c" name="package_ghostscript_9_07" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> | 4 <repository changeset_revision="10222a7db54c" name="package_ghostscript_9_07" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> |
| 8 </package> | 5 </package> |
| 9 <package name="graphicsmagick" version="1.3.18"> | 6 <package name="graphicsmagick" version="1.3.18"> |
| 10 <repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> | 7 <repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> |
| 11 </package> | 8 </package> |
| 9 <package name="r303" version="3.0.3"> | |
| 10 <repository changeset_revision="4c934f6b342e" name="package_r303" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> | |
| 11 </package> | |
| 12 <package name="biocbasics" version="2.14"> | 12 <package name="biocbasics" version="2.14"> |
| 13 <install version="1.0"> | 13 <install version="1.0"> |
| 14 <actions> | 14 <actions> |
| 15 <action type="set_environment_for_install"> | 15 <action type="set_environment_for_install"> |
| 16 <repository changeset_revision="826f08ed8859" name="package_r303" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/"> | 16 <repository changeset_revision="4c934f6b342e" name="package_r303" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/"> |
| 17 <package name="r303" version="3.0.3" /> | 17 <package name="r303" version="3.0.3" /> |
| 18 </repository> | 18 </repository> |
| 19 </action> | 19 </action> |
| 20 <action type="make_directory">$INSTALL_DIR</action> | 20 <action type="make_directory">$INSTALL_DIR</action> |
| 21 <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" > $INSTALL_DIR/runme.R</action> | 21 <action type="shell_command">echo "bioclite = 'http://bioconductor.org/biocLite.R'" > $INSTALL_DIR/runme.R</action> |
| 22 <action type="shell_command">echo "source(bioclite)" >> $INSTALL_DIR/runme.R</action> | |
| 22 <action type="shell_command">echo "installme=c('edgeR','limma','DESeq','DESeq2')" >> $INSTALL_DIR/runme.R</action> | 23 <action type="shell_command">echo "installme=c('edgeR','limma','DESeq','DESeq2')" >> $INSTALL_DIR/runme.R</action> |
| 23 <action type="shell_command">echo "biocLite()" >> $INSTALL_DIR/runme.R</action> | 24 <action type="shell_command">echo "biocLite()" >> $INSTALL_DIR/runme.R</action> |
| 24 <action type="shell_command">echo "biocLite(installme)" >> $INSTALL_DIR/runme.R</action> | 25 <action type="shell_command">echo "biocLite(installme)" >> $INSTALL_DIR/runme.R</action> |
| 25 <action type="shell_command">echo "install.packages(c('stringr','gplots'),dependencies=T,repos='http://cran.us.r-project.org')" >> $INSTALL_DIR/runme.R</action> | 26 <action type="shell_command">echo "install.packages(c('stringr','gplots'),dependencies=T,repos='http://cran.us.r-project.org')" >> $INSTALL_DIR/runme.R</action> |
| 26 <action type="shell_command">echo "quit(save='no')" >> $INSTALL_DIR/runme.R</action> | 27 <action type="shell_command">echo "quit(save='no')" >> $INSTALL_DIR/runme.R</action> |
| 27 <action type="shell_command">echo "PATH=$PATH 1>&2"</action> | 28 <action type="shell_command">echo "PATH=$PATH 1>&2"</action> |
| 28 <action type="shell_command">export PATH=$PATH && R CMD BATCH $INSTALL_DIR/runme.R </action> | 29 <action type="shell_command">echo "R_PATH=$R_PATH 1>&2"</action> |
| 30 <action type="shell_command">export PATH=$PATH && $R_PATH/R CMD BATCH $INSTALL_DIR/runme.R </action> | |
| 29 </actions> | 31 </actions> |
| 30 </install> | 32 </install> |
| 31 <readme>Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick (replaces imagemagick) and ghostscript for compressing R's bloated pdfs | 33 <readme>Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick (replaces imagemagick) and ghostscript for compressing R's bloated pdfs |
| 32 It's clunky but this is the most convenient way I could get anything installed into the package_r3 | 34 It's clunky but this is the most convenient way I could get anything installed into the package_r3 |
| 33 Note we use cran at fred hutch since no fastest mirror thingy | 35 Note we use cran at fred hutch since no fastest mirror thingy |