Mercurial > repos > kevyin > sometool
changeset 0:959a0e30d6c1 draft default tip
Uploaded
| author | kevyin |
|---|---|
| date | Sat, 19 Jan 2013 21:51:49 -0500 |
| parents | |
| children | |
| files | somewrapper.r somewrapper.xml tool_dependencies.xml |
| diffstat | 3 files changed, 43 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/somewrapper.r Sat Jan 19 21:51:49 2013 -0500 @@ -0,0 +1,3 @@ +library(DiffBind) + +print("somewrapper printing")
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/somewrapper.xml Sat Jan 19 21:51:49 2013 -0500 @@ -0,0 +1,19 @@ +<tool id="some_wrapper" name="diffbind" version="0.0.1"> + <requirements> + <requirement type="set_environment">SOMEWRAPPER_R_SCRIPT_PATH</requirement> + <requirement type="package" version="2.15.1">R</requirement> + </requirements> + <command interpreter="python"> + somewrapper.py Rscript \$SOMEWRAPPER_R_SCRIPT_PATH/somewrapper.r > ${some_out} + </command> + <inputs> + <param format="txt" name="input_file" type="data" label="some input" /> + </inputs> + <outputs> + <!--<data format="html" name="html_outfile" label="index" />--> + <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />--> + <data format="txt" name="some_out" label="S{tool.name} on #echo os.path.splitext(str($input_file.name))[0]#.zip" /> + </outputs> + <help> + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sat Jan 19 21:51:49 2013 -0500 @@ -0,0 +1,21 @@ +<?xml version="1.0"?> +<tool_dependency> + <set_environment version="1.0"> + <environment_variable name="SOMEWRAPPER_R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> + </set_environment> + <package name="R" version="2.15.1"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://CRAN.R-project.org/src/base/R-2/R-2.15.1.tar.gz</action> + <action type="shell_command">./configure --prefix=$INSTALL_DIR</action> + <action type="shell_command">make</action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> + You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build R. + </readme> + </package> +</tool_dependency>