Re: [galaxy-dev] Kallisto tool wrapper?
I’ll give it a shot.
Thanks for the tip.
brad
—
Brad Langhorst, Ph.D.
Development Scientist
New England Biolabs
On Apr 29, 2016, at 12:48 PM, Christian Brenninkmeijer
<christian.brenninkmei...@manchester.ac.uk<mailto:christian.brenninkmei...@manchester.ac.uk>>
wrote:
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<mailto:galaxy-dev-boun...@lists.galaxyproject.org>]
on behalf of Langhorst, Brad [langho...@neb.com<mailto:langho...@neb.com>]
Sent: Friday, April 29, 2016 5:30 PM
To: Anthony Bretaudeau
Cc:
galaxy-dev@lists.galaxyproject.org<mailto: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
On Apr 29, 2016, at 11:07 AM, Anthony Bretaudeau
<anthony.bretaud...@inria.fr<mailto:anthony.bretaud...@inria.fr>> wrote:
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...
On 29/04/2016 16:37, Lance Parsons wrote:
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.
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Re: [galaxy-dev] Kallisto tool wrapper?
Hmm.. Seems that Lior Patcher was OK with it, but the IUC still doesn't want to support the wrapper? That's a bit disappointing. Do people see issues with putting a wrapper for this on the public toolshed? And/or a package to install the dependency? Lance Björn Grüning wrote: Hi Lance, Kallisto has some licensing issues and the IUC decided to not offer it as IUC tool. Some related thread: https://groups.google.com/forum/#!topic/kallisto-sleuth-users/oVRg69Zmots Cheers, Bjoern Am 29.04.2016 um 16:37 schrieb Lance Parsons: 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. ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Kallisto tool wrapper?
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
On Apr 29, 2016, at 11:07 AM, Anthony Bretaudeau
<anthony.bretaud...@inria.fr<mailto:anthony.bretaud...@inria.fr>> wrote:
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...
On 29/04/2016 16:37, Lance Parsons wrote:
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.
___
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:
https://lists.galaxyproject.org/
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:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Kallisto tool wrapper?
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... On 29/04/2016 16:37, Lance Parsons wrote: 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. ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
