Mercurial > repos > fubar > edger_test
changeset 2:515a5e61874c draft
Uploaded
author | fubar |
---|---|
date | Wed, 12 Jun 2013 03:01:36 -0400 |
parents | 34cbb9e749da |
children | e22b0320a4ff |
files | rgedgeR/datatypes_conf_xml.sample rgedgeR/tool_dependencies.xml rgedgeR/tool_dependencies.xml~ |
diffstat | 3 files changed, 49 insertions(+), 3 deletions(-) [+] |
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--- a/rgedgeR/datatypes_conf_xml.sample Wed Jun 12 03:00:31 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -<datatype extension="gseagmt" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="true" mimetype="application/vnd.ms-excel"/> -<datatype extension="gseachip" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="true" mimetype="application/vnd.ms-excel"/>
--- a/rgedgeR/tool_dependencies.xml Wed Jun 12 03:00:31 2013 -0400 +++ b/rgedgeR/tool_dependencies.xml Wed Jun 12 03:01:36 2013 -0400 @@ -1,9 +1,10 @@ <?xml version="1.0"?> + +<tool_dependency> <!-- blame Boris - Ross stole it from his old 2.15 one --> -<tool_dependency> <package name="readline" version="6.2"> <repository name="package_readline_6_2" owner="boris" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> </package>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rgedgeR/tool_dependencies.xml~ Wed Jun 12 03:01:36 2013 -0400 @@ -0,0 +1,47 @@ + +<?xml version="1.0"?> +<!-- +blame Boris - Ross stole it from his old 2.15 one +--> +<tool_dependency> + <package name="readline" version="6.2"> + <repository name="package_readline_6_2" owner="boris" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + </package> + <package name="package_R" version="3.0.1"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://cran.ms.unimelb.edu.au/src/base/R-3/R-3.0.1.tar.gz</action> + <action type="set_environment_for_install"> + <repository name="package_readline_6_2" owner="boris" toolshed="http://testtoolshed.g2.bx.psu.edu/"> + <package name="readline" version="6.2" /> + </repository> + </action> + <action type="make_directory">$INSTALL_DIR</action> + <action type="shell_command">./configure --with-blas --with-lapack --enable-R-shlib --with-readline=no --with-x=no --prefix=$INSTALL_DIR && make && make install</action> + <action type="set_environment"> + <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable> + <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/lib/R/bin</environment_variable> + + </action> + </actions> + </install> + <readme>R is a free software environment for statistical computing and graphics + WARNING: See custom compilation options above + Modified from an older version of R by Boris by Ross Lazarus for R 3.0 + Added Bioc basics too + </readme> + </package> + <package name="package_BioCBasics" version="2.12"> + <install version="1.0"> + <actions> + <action type="shell_command">$INSTALL_DIR/lib/R/bin/R CMD BATCH installBioC.R </action> + </actions> + </install> + <readme>R is a free software environment for statistical computing and graphics + WARNING: See custom compilation options above + Modified from an older version of R by Boris by Ross Lazarus for R 3.0 + Added Bioc basics via this package installBioC.R script + </readme> + </package> +</tool_dependency>