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/
___
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/