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) ------------------------------------------------------------------------ This e-mail may contain confidential and/or privileged information. This information is intended only for the use of the individual(s) and entity(ies) to whom it is addressed. If you are the intended recipient, further disclosures are prohibited without proper authorization. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorized copying, disclosure or distribution of the material in this e-mail is strictly forbidden and possibly a violation of federal or state law and regulations. Baylor Health Care System, its subsidiaries, and affiliates hereby claim all applicable privileges related to this information. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/