Mercurial > repos > fubar > differential_count_models
diff tool_dependencies.xml @ 111:9f2e0ec3e826 draft
Uploaded
| author | fubar |
|---|---|
| date | Wed, 22 Oct 2014 23:37:31 -0400 |
| parents | d7e2a0c0cce9 |
| children | 525f2edd36d7 |
line wrap: on
line diff
--- a/tool_dependencies.xml Sun Jul 06 21:00:54 2014 -0400 +++ b/tool_dependencies.xml Wed Oct 22 23:37:31 2014 -0400 @@ -1,38 +1,50 @@ <?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 name="R_3_1_1" version="3.1.1"> + <repository changeset_revision="6ca21e466ef6" name="package_r_3_1_1" owner="fubar" 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="R" 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 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="biocbasics" version="2.14"> - <install version="1.0"> + <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="R" version="3.0.3" /> - </repository> + <action type="setup_r_environment"> + <repository changeset_revision="6ca21e466ef6" name="package_r_3_1_1" owner="fubar" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="R_3_1_1" version="3.1.1" /> + </repository> + <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/AnnotationDbi_1.26.1.tar.gz</package> + <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/Biobase_2.24.0.tar.gz</package> + <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/BiocGenerics_0.10.0.tar.gz</package> + <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/DBI_0.3.1.tar.gz</package> + <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/DESeq2_1.4.5.tar.gz</package> + <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/GenomicRanges_1.16.4.tar.gz</package> + <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/IRanges_1.22.10.tar.gz</package> + <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/RColorBrewer_1.0-5.tar.gz</package> + <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/RSQLite_0.11.4.tar.gz</package> + <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/RcppArmadillo_0.4.450.1.0.tar.gz</package> + <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/Rcpp_0.11.3.tar.gz</package> + <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/XML_3.98-1.1.tar.gz</package> + <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/annotate_1.42.1.tar.gz</package> + <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/edgeR_3.6.8.tar.gz</package> + <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/genefilter_1.46.1.tar.gz</package> + <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/getopt_1.20.0.tar.gz</package> + <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/ggplot2_1.0.0.tar.gz</package> + <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/limma_3.20.9.tar.gz</package> + <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/locfit_1.5-9.1.tar.gz</package> + <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/reshape2_1.4.tar.gz</package> + <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rjson_0.2.14.tar.gz</package> + <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/xtable_1.7-4.tar.gz</package> </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\")" >> $INSTALL_DIR/runme.R</action> - <action type="shell_command">export PATH=$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> + <readme> + Differential gene expression analysis + Ubuntu has a bug with libgfortran. To fix that create a symlink like: sudo ln -s /usr/lib/x86_64-linux-gnu/libgfortran.so.3 /usr/lib/x86_64-linux-gnu/libgfortran.so + </readme> </package> </tool_dependency>