| Next changeset 1:e6171a39dd04 (2014-11-06) |
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Commit message:
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added:
INSTALL.r tool_dependencies.xml |
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| diff -r 000000000000 -r d57322d79cfe INSTALL.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/INSTALL.r Thu Nov 06 16:04:57 2014 +0100 |
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| @@ -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/") + |
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| diff -r 000000000000 -r d57322d79cfe tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Nov 06 16:04:57 2014 +0100 |
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| @@ -0,0 +1,44 @@ +<?xml version="1.0"?> +<tool_dependency> +<!-- see also http://wiki.galaxyproject.org/ToolShedToolFeatures for syntax help + partly based on : https://toolshed.g2.bx.psu.edu/repos/iuc/package_r_3_0_3 + --> + <package name="R_bioc_metams" version="3.1.1"> + <install version="1.0"> + <actions_group> + <actions> + <action type="download_by_url">http://cran.r-project.org/src/base/R-3/R-3.1.1.tar.gz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + <action type="shell_command"> + cd $INSTALL_DIR; $INSTALL_DIR/configure --libdir=$INSTALL_DIR/lib --prefix=$INSTALL_DIR + </action> + <action type="shell_command">make -C $INSTALL_DIR</action> + </actions> + <action type="set_environment"> + <environment_variable action="set_to" name="R_DOC_DIR">$INSTALL_DIR/doc</environment_variable> + <environment_variable action="set_to" name="R_HOME_DIR">$INSTALL_DIR</environment_variable> + <environment_variable action="set_to" name="R_INCLUDE_DIR">$INSTALL_DIR/include</environment_variable> + <environment_variable action="set_to" name="R_SHARE_DIR">$INSTALL_DIR/share</environment_variable> + <environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable> + <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR</environment_variable> + <environment_variable action="set_to" name="RHOME">$INSTALL_DIR</environment_variable> + <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/library</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + </action> + <!-- the Bioconductor and metaMS part --> + <action type="shell_command">wget -P $INSTALL_DIR http://toolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_metabolomics_r_dependencies/raw-file/tip/INSTALL.r</action> + <action type="shell_command">$INSTALL_DIR/bin/Rscript $INSTALL_DIR/INSTALL.r</action> + </actions_group> + </install> + <readme> + Ensures R 3.1.1 is installed. + Ensures Bioconductor 3.0 and package metaMS, multtest and snow are installed. + R is a free software environment for statistical computing and graphics. + </readme> + </package> + + +</tool_dependency> \ No newline at end of file |