Mercurial > repos > fubar > differential_count_models
comparison tool_dependencies.xml @ 111:9f2e0ec3e826 draft
Uploaded
| author | fubar |
|---|---|
| date | Wed, 22 Oct 2014 23:37:31 -0400 |
| parents | d7e2a0c0cce9 |
| children | 525f2edd36d7 |
comparison
equal
deleted
inserted
replaced
| 110:d7e2a0c0cce9 | 111:9f2e0ec3e826 |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | 2 <tool_dependency> |
| 3 <package name="ghostscript" version="9.10"> | 3 <package name="R_3_1_1" version="3.1.1"> |
| 4 <repository changeset_revision="9345d2740f0c" name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> | 4 <repository changeset_revision="6ca21e466ef6" name="package_r_3_1_1" owner="fubar" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> |
| 5 </package> | 5 </package> |
| 6 <package name="graphicsmagick" version="1.3.18"> | 6 <package name="graphicsmagick" version="1.3.18"> |
| 7 <repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> | 7 <repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> |
| 8 </package> | 8 </package> |
| 9 <package name="R" version="3.0.3"> | 9 <package name="ghostscript" version="9.10"> |
| 10 <repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> | 10 <repository changeset_revision="9345d2740f0c" name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> |
| 11 </package> | 11 </package> |
| 12 | |
| 12 <package name="biocbasics" version="2.14"> | 13 <package name="biocbasics" version="2.14"> |
| 13 <install version="1.0"> | 14 <install version="1.0"> |
| 14 <actions> | 15 <actions> |
| 15 <action type="set_environment_for_install"> | 16 <action type="setup_r_environment"> |
| 16 <repository changeset_revision="9ff23e0b280b" name="package_r_3_0_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> | 17 <repository changeset_revision="6ca21e466ef6" name="package_r_3_1_1" owner="fubar" toolshed="https://testtoolshed.g2.bx.psu.edu"> |
| 17 <package name="R" version="3.0.3" /> | 18 <package name="R_3_1_1" version="3.1.1" /> |
| 18 </repository> | 19 </repository> |
| 20 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/AnnotationDbi_1.26.1.tar.gz</package> | |
| 21 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/Biobase_2.24.0.tar.gz</package> | |
| 22 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/BiocGenerics_0.10.0.tar.gz</package> | |
| 23 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/DBI_0.3.1.tar.gz</package> | |
| 24 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/DESeq2_1.4.5.tar.gz</package> | |
| 25 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/GenomicRanges_1.16.4.tar.gz</package> | |
| 26 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/IRanges_1.22.10.tar.gz</package> | |
| 27 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/RColorBrewer_1.0-5.tar.gz</package> | |
| 28 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/RSQLite_0.11.4.tar.gz</package> | |
| 29 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/RcppArmadillo_0.4.450.1.0.tar.gz</package> | |
| 30 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/Rcpp_0.11.3.tar.gz</package> | |
| 31 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/XML_3.98-1.1.tar.gz</package> | |
| 32 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/annotate_1.42.1.tar.gz</package> | |
| 33 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/edgeR_3.6.8.tar.gz</package> | |
| 34 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/genefilter_1.46.1.tar.gz</package> | |
| 35 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/getopt_1.20.0.tar.gz</package> | |
| 36 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/ggplot2_1.0.0.tar.gz</package> | |
| 37 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/limma_3.20.9.tar.gz</package> | |
| 38 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/locfit_1.5-9.1.tar.gz</package> | |
| 39 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/reshape2_1.4.tar.gz</package> | |
| 40 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rjson_0.2.14.tar.gz</package> | |
| 41 <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/xtable_1.7-4.tar.gz</package> | |
| 19 </action> | 42 </action> |
| 20 <action type="make_directory">$INSTALL_DIR</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> | |
| 23 <action type="shell_command">echo "installme=c(\"edgeR\",\"limma\",\"DESeq\",\"DESeq2\")" >> $INSTALL_DIR/runme.R</action> | |
| 24 <action type="shell_command">echo "biocLite()" >> $INSTALL_DIR/runme.R</action> | |
| 25 <action type="shell_command">echo "biocLite(installme)" >> $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> | |
| 27 <action type="shell_command">echo "quit(save=\"no\")" >> $INSTALL_DIR/runme.R</action> | |
| 28 <action type="shell_command">export PATH=$PATH && R CMD BATCH $INSTALL_DIR/runme.R </action> | |
| 29 </actions> | 43 </actions> |
| 30 </install> | 44 </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 | 45 <readme> |
| 32 It's clunky but this is the most convenient way I could get anything installed into the package_r3 | 46 Differential gene expression analysis |
| 33 Note we use cran at fred hutch since no fastest mirror thingy | 47 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 |
| 34 If atlas will not compile - eg: it thinks autoscaling is on or something, | 48 </readme> |
| 35 you need (eg for ubuntu) libopenblas-base installed on all nodes after commenting or removing all atlas references | |
| 36 </readme> | |
| 37 </package> | 49 </package> |
| 38 </tool_dependency> | 50 </tool_dependency> |