Mercurial > repos > deepakjadmin > limmatest
changeset 0:31eb67db059b draft default tip
Uploaded
| author | deepakjadmin |
|---|---|
| date | Wed, 23 Sep 2015 05:54:53 -0400 |
| parents | |
| children | |
| files | testing.xml tool_dependencies.xml |
| diffstat | 2 files changed, 53 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/testing.xml Wed Sep 23 05:54:53 2015 -0400 @@ -0,0 +1,15 @@ +<tool id="kunv02rt90uis" name="R-3-2-0" version="1.0.0"> + <description>R version and installation test</description> +<requirements> + <requirement type="set_environment">R_ROOT_DIR</requirement> + <requirement type="package" version="3.2.0">R</requirement> +</requirements> + <command> /bin/which R > $output_file; + /bin/which \$R_ROOT_DIR/bin/R >> $output_file; + echo \$R_ROOT_DIR >> $output_file; + echo \$PATH >> $output_file; + </command> + <outputs> + <data type="data" format="txt" name="output_file" label ="output_r_3_2_0.env" /> + </outputs> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Sep 23 05:54:53 2015 -0400 @@ -0,0 +1,38 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="R" version="3.2.0"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://cran.r-project.org/src/base/R-3/R-3.2.0.tar.gz</action> + <action type="shell_command">./configure</action> + <action type="shell_command">make</action> + <action type="shell_command">make install</action> + <action type="move_file"> + <source>R.3.2.0</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + <readme> +R-3.2.0 installed now try edgeR + </readme> + </package> + <package name="limma" version="3.24.12"> + <install version="1.0"> + <actions> + <action type="setup_r_environment"> + <package name="R" version="3.2.0" /> + <action type="download_by_url">http://bioconductor.org/packages/release/bioc/src/contrib/limma_3.24.12.tar.gz</action> + <action type="shell_command">R CMD INSTALL limma_3.24.12.tar.gz</action> + </action> + </actions> + </install> + <readme> +limma_3.24.12 installed now try edgeR + </readme> + </package> + +</tool_dependency>