Brandi,

The cufflinks tools are now available on the main Galaxy tool shed:

http://toolshed.g2.bx.psu.edu/view/devteam/all_cufflinks_tool_suite

Installing this repository into your Galaxy instance will pull in the versions of the tools that were originally distributed with the Galaxy codebase. There are however updated versions of these tools available on the same tool shed, at the following locations:

http://toolshed.g2.bx.psu.edu/view/devteam/cuffcompare
http://toolshed.g2.bx.psu.edu/view/devteam/cuffdiff
http://toolshed.g2.bx.psu.edu/view/devteam/cufflinks
http://toolshed.g2.bx.psu.edu/view/devteam/cuffmerge

For details on how to install these repositories into your Galaxy instance, see the following wiki page:

https://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy

 --Dave B.

On 2014-01-13 22:06, Cantarel, Brandi L. wrote:
A colleague has asked me to set up a galaxy server for purpose of
running tophat/cufflinks.
A recent paper in BMC Genomics would indicate that those tools are
integrated into Galaxy.

When I download (hg clone) the distribution, I only see tophat, but none
of the other tuxedo software.  The funny thing that is I google
bitbucket, cufflinks, galaxy — I can find a few XML files to run the
software but I can’t figure out how to get those files into my local
install…I tried the stable and default distribution, but neither
included these files…


Is there something that I am missing in the download for the ngs-rna tools?

Thanks!
Brandi Cantarel


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Brandi Cantarel, PhD
Bioinformatics Research Scientist
Baylor Institute for Immunology Research
Baylor Health Care System
214-818-8673 (office)



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