Kallisto tool wrapper?

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Kallisto tool wrapper?

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.

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

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Kallisto tool wrapper?

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.

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


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Re: Kallisto tool wrapper?

Anthony Bretaudeau-2
In reply to this post by Lance Parsons
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: Kallisto tool wrapper?

Langhorst, Brad
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 <[hidden email]> 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: Kallisto tool wrapper?

Björn Grüning-3
In reply to this post by Lance Parsons
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.
>
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Re: Kallisto tool wrapper?

Christian Brenninkmeijer
In reply to this post by Langhorst, Brad
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 [[hidden email]] on behalf of Langhorst, Brad [[hidden email]]
Sent: Friday, April 29, 2016 5:30 PM
To: Anthony Bretaudeau
Cc: [hidden email]
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 <[hidden email]> 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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in your mail client.  To manage your subscriptions to this
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Re: Kallisto tool wrapper?

Lance Parsons
In reply to this post by Björn Grüning-3
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
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Re: Kallisto tool wrapper?

Langhorst, Brad
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

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 <[hidden email]> 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/


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Re: Kallisto tool wrapper?

Langhorst, Brad
In reply to this post by Christian Brenninkmeijer
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 <[hidden email]> 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 [[hidden email]] on behalf of Langhorst, Brad [[hidden email]]
Sent: Friday, April 29, 2016 5:30 PM
To: Anthony Bretaudeau
Cc: [hidden email]
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 <[hidden email]> 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/


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Re: Kallisto tool wrapper?

Lance Parsons
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).

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"
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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 [[hidden email]] on behalf of Langhorst, Brad [[hidden email]]
Sent: Friday, April 29, 2016 5:30 PM
To: Anthony Bretaudeau
Cc: [hidden email]
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:
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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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in your mail client. To manage your subscriptions to this
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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"
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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


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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