Mercurial > repos > fubar > differential_count_models
comparison tool_dependencies.xml @ 70:e4291e5a03c1 draft
Uploaded
| author | fubar |
|---|---|
| date | Tue, 18 Feb 2014 01:07:24 -0500 |
| parents | 919822102c86 |
| children | f33aac17f15d |
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| 69:919822102c86 | 70:e4291e5a03c1 |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | 2 <tool_dependency> |
| 3 <package name="r302" version="3.0.2"> | 3 <package name="r302" version="3.0.2"> |
| 4 <repository changeset_revision="ce4a3c48dbd7" name="package_r302" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> | 4 <repository changeset_revision="c161b72d384e" name="package_r302" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> |
| 5 </package> | 5 </package> |
| 6 <package name="ghostscript" version="9.10"> | 6 <package name="ghostscript" version="9.10"> |
| 7 <repository changeset_revision="9345d2740f0c" name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> | 7 <repository changeset_revision="9345d2740f0c" name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> |
| 8 </package> | 8 </package> |
| 9 <package name="graphicsmagick" version="1.3.18"> | 9 <package name="graphicsmagick" version="1.3.18"> |
| 11 </package> | 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="ce4a3c48dbd7" name="package_r302" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/"> | 16 <repository changeset_revision="c161b72d384e" name="package_r302" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/"> |
| 17 <package name="r302" version="3.0.2" /> | 17 <package name="r302" version="3.0.2" /> |
| 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 "source('http://bioconductor.org/biocLite.R')" > $INSTALL_DIR/runme.R</action> |
| 22 <action type="shell_command">echo "installme=c('edgeR','limma','DESeq','DESeq2')" >> $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 "biocLite()" >> $INSTALL_DIR/runme.R</action> | 23 <action type="shell_command">echo "biocLite()" >> $INSTALL_DIR/runme.R</action> |
| 24 <action type="shell_command">echo "biocLite(installme)" >> $INSTALL_DIR/runme.R</action> | 24 <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> | 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 "quit(save='no')" >> $INSTALL_DIR/runme.R</action> | 26 <action type="shell_command">echo "quit(save='no')" >> $INSTALL_DIR/runme.R</action> |
| 27 <action type="shell_command"> export PATH=$PATH && export R_HOME=$R_HOME && export R_LIBS=$R_LIBS && $R_PATH/R CMD BATCH $INSTALL_DIR/runme.R </action> | 27 <action type="shell_command" /> |
| 28 <action type="shell_command"> export PATH=$PATH && echo "PATH=$PATH" && export R_HOME=$R_HOME && export R_LIBS=$R_LIBS && R CMD BATCH $INSTALL_DIR/runme.R </action> | |
| 28 </actions> | 29 </actions> |
| 29 </install> | 30 </install> |
| 30 <readme>Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick (replaces imagemagick) and ghostscript for compressing R's bloated pdfs | 31 <readme>Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick (replaces imagemagick) and ghostscript for compressing R's bloated pdfs |
| 31 It's clunky but this is the most convenient way I could get anything installed into the package_r3 | 32 It's clunky but this is the most convenient way I could get anything installed into the package_r3 |
| 32 Note we use cran at fred hutch since no fastest mirror thingy | 33 Note we use cran at fred hutch since no fastest mirror thingy |