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Welcome to project brs2010p29

Mailing lists

This project provides the following mailing lists.

Source access

If available, anonymous readonly subversion access works as follows:

  svn co https://trac.nbic.nl/svn/brs2010p29 brs2010p29

Write access is only available to registered developers.

You can become a developer by registering yourself if you haven't already done so, and requesting write access on the brs2010p29-users mailing list.

Starting Points

Other NBIC software projects

All active NBIC software projects can be accessed from the project index.


Installation of PhyloProfiler

This section describes the installation procedure for the PhyloProfiler Galaxy tools.

Requirements

R packages

LaTeX packages

The following LaTeX packages were installed (extracted using dpkg --get-selections | grep tex). Note however that not all packages might be required. As a strategy please firstly follow the OS guide for installing LaTeX, testing the software and install further packages based on possible error messages.

texinfo
texlive

and can be installed with sudo apt-get install texinfo texlive on Ubuntu or Debian systems.

Testing LaTeX

Included is a 'test' directory containing testTex.sh. Please see the included README.txt file for instructions. If this test succeeds, a PDF file is produced in the output folder with a report on the given data.

Galaxy Tool Installation

  • Checkout from SVN in the Galaxy tools folder:
    cd galaxy-central/tools
    svn co [https://trac.nbic.nl/svn/brs2010p29/trunk/] phyloprofiler
    

The PhyloProfiler tools run R scripts for processing the data for which R needs to know where the actual scripts are (phyloprofiler/rscipts). Therefore, please note the absolute location of the installation location (such as galaxy-central/tools/phyloprofiler as used above) and change the path in all XML files to reflect the location:

  • report.xml on line 4
  • filter_data.xml on line 5
  • compare_subsets.xml on line 4
  • dataconv.xml seem to have missed this update, will be tested
  • Add the following section to Galaxy's tool_conf.xml:
    <section name="PhyloProfiler” id=”phyloprofiler”>
        <tool file=”phyloprofiler/dataconv.xml” />
        <tool file=”phyloprofiler/filter_data.xml” />
        <tool file=”phyloprofiler/compare_subsets.xml” />
        <tool file=”phyloprofiler/report.xml” />
    </section>
    
  • This added the list of PhyloProfiler tools to the Galaxy tool menu
  • Editing the tool_conf.xml file requires a restart of Galaxy
  • Verify that the PhyloProfiler section has been added to the tool menu after the restart
Last modified 4 years ago Last modified on Apr 11, 2014, 3:53:13 PM