GalaxyInstall

To install into an existing Galaxy installation

Download the tool as a pre-packaged Galaxy folder

1. Decompress the folder from the tar.gz

   -zxvf qPMerge-version.tar.gz

2. Add the qPMerge folder to the tools folder within your galaxy installation

3. Add qPMerge_tool_conf.xml to the tool_config_file option in universe_wsgi.ini (found in the base directory of Galaxy). For example a typical line in universe_wsgi.ini might read:

   tool_config_file = tool_conf.xml,shed_tool_conf.xml,tools/qPMerge/qPMerge_tool_conf.xml

4. Restart your galaxy instance

Optionally an installation of R with JRI is required for some of the methods in the statistics package. You will need to have the following variables set (obviously adjust the values to the directories where you have installed these libraries).

export JRI_LIB_HOME='/rpacks/rJava/jri'
export R_LIBS=rpacks
export R_HOME=R-devel

It would be useful to have the following packages installed in R (most are only required when qPMerge is called as a library)

install.packages('equivalence"')
install.packages('VennDiagram')
install.packages('gplots')
install.packages('pvclust')