Kallisto tool wrapper?
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
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
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.
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.bretaudeau@inria.fr<mailto:anthony.bretaudeau@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/
Have a look at: https://github.com/galaxyproject/galaxy/blob/master/lib/galaxy/tools/deps/re... 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-bounces@lists.galaxyproject.org] on behalf of Langhorst, Brad [Langhorst@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.bretaudeau@inria.fr<mailto:anthony.bretaudeau@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/
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.brenninkmeijer@manchester.ac.uk<mailto:christian.brenninkmeijer@manchester.ac.uk>> wrote: Have a look at: https://github.com/galaxyproject/galaxy/blob/master/lib/galaxy/tools/deps/re... 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-bounces@lists.galaxyproject.org<mailto:galaxy-dev-bounces@lists.galaxyproject.org>] on behalf of Langhorst, Brad [Langhorst@neb.com<mailto:Langhorst@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.bretaudeau@inria.fr<mailto:anthony.bretaudeau@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/
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:Langhorst@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
___________________________________________________________ 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/ Christian Brenninkmeijer <mailto:christian.brenninkmeijer@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/re...
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-bounces@lists.galaxyproject.org] on behalf of Langhorst, Brad [Langhorst@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
___________________________________________________________ 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/ Langhorst, Brad <mailto:Langhorst@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
___________________________________________________________ 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/ Anthony Bretaudeau <mailto:anthony.bretaudeau@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...
___________________________________________________________ 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/ Lance Parsons <mailto:lparsons@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
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.
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.
Hi Lance: I did not hear anything about a license change for Kallisto - it still says something like talk to our laywers for commercial use on their web site https://pachterlab.github.io/kallisto/license I’ve been using salmon for a few months now and find that it’s very good, though it is always nice to have more angles to look at data. brad — Brad Langhorst, Ph.D. Development Scientist New England Biolabs On Apr 29, 2016, at 1:10 PM, Lance Parsons <lparsons@princeton.edu<mailto:lparsons@princeton.edu>> wrote: 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/
participants (5)
-
Anthony Bretaudeau -
Björn Grüning -
Christian Brenninkmeijer -
Lance Parsons -
Langhorst, Brad