Just realized that you've already started work on a Salmon wrapper, thanks! It does look like a very similar tool. I'd be happy to help out with that effort instead of Kallisto if that's what the community wants (and researchers are happy enough using Salmon vs. Kallisto).

Langhorst, Brad <mailto:langho...@neb.com>
April 29, 2016 at 2:11 PM
I’ll give it a shot.
Thanks for the tip.


brad
—
Brad Langhorst, Ph.D.
Development Scientist
New England Biolabs





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Christian Brenninkmeijer <mailto:christian.brenninkmei...@manchester.ac.uk>
April 29, 2016 at 12:48 PM
Have a look at:
https://github.com/galaxyproject/galaxy/blob/master/lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py

This will attempt to find any dependencies previously install from a toolshed to use in Planemo.

Christian

PS.
If your package is not exactly named you may have to comment out the condition
if package_name.lower().startswith("package_" + name.lower()):



------------------------------------------------------------------------
*From:* galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of Langhorst, Brad [langho...@neb.com]
*Sent:* Friday, April 29, 2016 5:30 PM
*To:* Anthony Bretaudeau
*Cc:* galaxy-dev@lists.galaxyproject.org
*Subject:* Re: [galaxy-dev] Kallisto tool wrapper?

Salmon works in a similar way to kallisto.
I’ve been tweaking the test toolshed wrapper of that lately, but I have not yet figured out how to get planemo to test it properly - as soon as I do i’ll publish it to the toolshed.


Brad
—
Brad Langhorst, Ph.D.
Development Scientist
New England Biolabs





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Langhorst, Brad <mailto:langho...@neb.com>
April 29, 2016 at 12:30 PM
Salmon works in a similar way to kallisto.
I’ve been tweaking the test toolshed wrapper of that lately, but I have not yet figured out how to get planemo to test it properly - as soon as I do i’ll publish it to the toolshed.


Brad
—
Brad Langhorst, Ph.D.
Development Scientist
New England Biolabs





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Anthony Bretaudeau <mailto:anthony.bretaud...@inria.fr>
April 29, 2016 at 11:07 AM
Hi,

While working on Trinity, I made a package (but no wrapper) for it in IUC: https://github.com/galaxyproject/tools-iuc/pull/613

It is not yet merged because of a licence problem though...




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Lance Parsons <mailto:lpars...@princeton.edu>
April 29, 2016 at 10:37 AM
I've had requests from users to install Kallisto as Galaxy tool. I didn't see any wrappers or evidence of wrappers in my searching, but I thought I'd ask here to see if anyone is working on or interested in working on such a thing.


--
Lance Parsons - Scientific Programmer
Carl C. Icahn Laboratory - Room 136
Lewis-Sigler Institute for Integrative Genomics
Princeton University

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