Mercurial > repos > pieterlukasse > prims_metabolomics
changeset 6:dee3302c1ed0
moved bioconductor part
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Thu, 06 Nov 2014 10:50:02 +0100 |
| parents | 128509e27429 |
| children | 504be42b4927 |
| files | INSTALL.r tool_dependencies.xml |
| diffstat | 2 files changed, 26 insertions(+), 3 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/INSTALL.r Thu Nov 06 10:50:02 2014 +0100 @@ -0,0 +1,16 @@ +# get R http://cran.r-project.org/src/base/R-3/R-3.0.3.tar.gz + +# installs Bioconductor +source("http://bioconductor.org/biocLite.R") +biocLite() + +# upgrage? Some packages are "old" and can be upgraded with: biocLite("BiocUpgrade") + + +# install metaMS and multtest for differential analysis tool (from xcms) +biocLite("metaMS") +biocLite("multtest") + +# for "multi-threading" (actually starts multiple R processes for parallel processing): +install.packages("snow", repos="http://cran.rstudio.com/") +
--- a/tool_dependencies.xml Fri Oct 24 17:03:39 2014 +0200 +++ b/tool_dependencies.xml Thu Nov 06 10:50:02 2014 +0100 @@ -3,12 +3,19 @@ <!-- see also http://wiki.galaxyproject.org/ToolShedToolFeatures for syntax help --> <package name="R_bioc_metams" version="3.1.1"> - <repository changeset_revision="71356c62e5cd" name="prims_metabolomics_dependencies" owner="pieterlukasse" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="0af753942e7b" name="prims_metabolomics_dependencies" owner="pieterlukasse" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <install version="1.0"> + <actions_group> + <!-- the Bioconductor and metaMS part --> + <action type="shell_command">wget -P $INSTALL_DIR http://testtoolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_metabolomics/raw-file/tip/INSTALL.r</action> + <action type="shell_command">$R_ROOT_DIR/bin/Rscript $INSTALL_DIR/INSTALL.r</action> + </actions_group> + </install> + </package> <readme> This dependency: - Ensures R 3.1.1 is installed. + Ensures R 3.1.1 installation is triggered (via dependency). Ensures Bioconductor 3.0 and package metaMS, multtest and snow are installed. - R is a free software environment for statistical computing and graphics. </readme> </tool_dependency> \ No newline at end of file