Re: [galaxy-dev] Proteomics category on main toolshed?
Thanks Ira, Just so you know, the Galaxy functional test framework now supports testing installed tools if the repository tools include tests and test datasets are included in the repository in a test-data subdirectory. Here is the relevant section of the tool shed wiki describing this: http://wiki.g2.bx.psu.edu/Tool%20Shed#Using_Galaxy.27s_functional_test_frame... Greg On Mar 29, 2012, at 6:53 PM, Ira Cooke wrote:
Dear Greg,
Thanks very much for that. I'll do a last proof-read of the tools and upload later on today.
We're working on some better documentation ... to get it all working takes some extra setup steps on the part of the user.
Ira
On 30/03/2012, at 9:49 AM, Greg Von Kuster wrote:
Hello Ira,
I've added the category to the main tool shed. Thanks for the request and your upcoming contributions!
Greg Von Kuster
On Mar 29, 2012, at 5:33 PM, Ira Cooke wrote:
Dear list,
I would like to add a suite of proteomics tools to the toolshed but there is currently no suitable category.
Would it be possible to add a category called Proteomics?
Thanks Ira
Thanks ... that would definitely be a good idea. Well try to implement proper tests for all the tools. Ira On 30/03/2012, at 10:01 AM, Greg Von Kuster wrote:
Thanks Ira,
Just so you know, the Galaxy functional test framework now supports testing installed tools if the repository tools include tests and test datasets are included in the repository in a test-data subdirectory. Here is the relevant section of the tool shed wiki describing this:
http://wiki.g2.bx.psu.edu/Tool%20Shed#Using_Galaxy.27s_functional_test_frame...
Greg
On Mar 29, 2012, at 6:53 PM, Ira Cooke wrote:
Dear Greg,
Thanks very much for that. I'll do a last proof-read of the tools and upload later on today.
We're working on some better documentation ... to get it all working takes some extra setup steps on the part of the user.
Ira
On 30/03/2012, at 9:49 AM, Greg Von Kuster wrote:
Hello Ira,
I've added the category to the main tool shed. Thanks for the request and your upcoming contributions!
Greg Von Kuster
On Mar 29, 2012, at 5:33 PM, Ira Cooke wrote:
Dear list,
I would like to add a suite of proteomics tools to the toolshed but there is currently no suitable category.
Would it be possible to add a category called Proteomics?
Thanks Ira
Hi Greg, I'm afraid to say I might have been a bit ahead of myself in asking you to create that Proteomics category. We're almost ready to upload our tools, but at the last minute we've discovered a bunch of issues we need to sort out. I'm going away for Easter and won't be back until the 16th ... so I guess the earliest our tools would be up is after the 16th. Sorry about that. I hope you're OK with a 0 beside the Proteomics category for now. Ira On 30/03/2012, at 10:03 AM, Ira Cooke wrote:
Thanks ... that would definitely be a good idea.
Well try to implement proper tests for all the tools.
Ira
On 30/03/2012, at 10:01 AM, Greg Von Kuster wrote:
Thanks Ira,
Just so you know, the Galaxy functional test framework now supports testing installed tools if the repository tools include tests and test datasets are included in the repository in a test-data subdirectory. Here is the relevant section of the tool shed wiki describing this:
http://wiki.g2.bx.psu.edu/Tool%20Shed#Using_Galaxy.27s_functional_test_frame...
Greg
On Mar 29, 2012, at 6:53 PM, Ira Cooke wrote:
Dear Greg,
Thanks very much for that. I'll do a last proof-read of the tools and upload later on today.
We're working on some better documentation ... to get it all working takes some extra setup steps on the part of the user.
Ira
On 30/03/2012, at 9:49 AM, Greg Von Kuster wrote:
Hello Ira,
I've added the category to the main tool shed. Thanks for the request and your upcoming contributions!
Greg Von Kuster
On Mar 29, 2012, at 5:33 PM, Ira Cooke wrote:
Dear list,
I would like to add a suite of proteomics tools to the toolshed but there is currently no suitable category.
Would it be possible to add a category called Proteomics?
Thanks Ira
No worries, Ira - have a great Easter vacation! On Apr 3, 2012, at 7:20 AM, Ira Cooke wrote:
Hi Greg,
I'm afraid to say I might have been a bit ahead of myself in asking you to create that Proteomics category. We're almost ready to upload our tools, but at the last minute we've discovered a bunch of issues we need to sort out. I'm going away for Easter and won't be back until the 16th ... so I guess the earliest our tools would be up is after the 16th.
Sorry about that. I hope you're OK with a 0 beside the Proteomics category for now.
Ira
On 30/03/2012, at 10:03 AM, Ira Cooke wrote:
Thanks ... that would definitely be a good idea.
Well try to implement proper tests for all the tools.
Ira
On 30/03/2012, at 10:01 AM, Greg Von Kuster wrote:
Thanks Ira,
Just so you know, the Galaxy functional test framework now supports testing installed tools if the repository tools include tests and test datasets are included in the repository in a test-data subdirectory. Here is the relevant section of the tool shed wiki describing this:
http://wiki.g2.bx.psu.edu/Tool%20Shed#Using_Galaxy.27s_functional_test_frame...
Greg
On Mar 29, 2012, at 6:53 PM, Ira Cooke wrote:
Dear Greg,
Thanks very much for that. I'll do a last proof-read of the tools and upload later on today.
We're working on some better documentation ... to get it all working takes some extra setup steps on the part of the user.
Ira
On 30/03/2012, at 9:49 AM, Greg Von Kuster wrote:
Hello Ira,
I've added the category to the main tool shed. Thanks for the request and your upcoming contributions!
Greg Von Kuster
On Mar 29, 2012, at 5:33 PM, Ira Cooke wrote:
Dear list,
I would like to add a suite of proteomics tools to the toolshed but there is currently no suitable category.
Would it be possible to add a category called Proteomics?
Thanks Ira
Ira, As part of your Proteomics Toolshed, are you thinking of making some Protein databases available ? Latest UniProt/SwissProt (~ 250 MB) or UniProt/TREMBl (~ 8GB) ? That could be very helpful for future Proteomics tools we are developing. http://en.wikipedia.org/wiki/UniProt Also, could it go in the Galaxy Cloudman /mnt/galaxyIndices volume ? That's a question for the Galaxy team I think. Rgds, Greg E On Tue, Apr 3, 2012 at 11:33 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
No worries, Ira - have a great Easter vacation!
On Apr 3, 2012, at 7:20 AM, Ira Cooke wrote:
Hi Greg,
I'm afraid to say I might have been a bit ahead of myself in asking you to create that Proteomics category. We're almost ready to upload our tools, but at the last minute we've discovered a bunch of issues we need to sort out. I'm going away for Easter and won't be back until the 16th ... so I guess the earliest our tools would be up is after the 16th.
Sorry about that. I hope you're OK with a 0 beside the Proteomics category for now.
Ira
On 30/03/2012, at 10:03 AM, Ira Cooke wrote:
Thanks ... that would definitely be a good idea.
Well try to implement proper tests for all the tools.
Ira
On 30/03/2012, at 10:01 AM, Greg Von Kuster wrote:
Thanks Ira,
Just so you know, the Galaxy functional test framework now supports testing installed tools if the repository tools include tests and test datasets are included in the repository in a test-data subdirectory. Here is the relevant section of the tool shed wiki describing this:
http://wiki.g2.bx.psu.edu/Tool%20Shed#Using_Galaxy.27s_functional_test_frame...
Greg
On Mar 29, 2012, at 6:53 PM, Ira Cooke wrote:
Dear Greg,
Thanks very much for that. I'll do a last proof-read of the tools
We're working on some better documentation ... to get it all working
takes some extra setup steps on the part of the user.
Ira
On 30/03/2012, at 9:49 AM, Greg Von Kuster wrote:
Hello Ira,
I've added the category to the main tool shed. Thanks for the
request and your upcoming contributions!
Greg Von Kuster
On Mar 29, 2012, at 5:33 PM, Ira Cooke wrote:
> Dear list, > > I would like to add a suite of proteomics tools to the toolshed but
and upload later on today. there is currently no suitable category.
> > Would it be possible to add a category called Proteomics? > > Thanks > Ira
___________________________________________________________ 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:
-- Greg Edwards, Port Jackson Bioinformatics gedwards2@gmail.com
Hi Greg, I'm not too sure of the best way to make these available (perhaps showing by ignorance of the way Galaxy handles such databases in the genomics world). We've got a set of commandline tools which support protk-toolshed https://bitbucket.org/iracooke/protk And included among these is a tool "manage_db" which makes it relatively easy to setup a database for proteomics .. and then update it regularly. The tools also support using a FASTA file in your history as a database for a proteomics search. We need quite a large variety of custom databases (eg subsets of Swissprot for different taxa) because some search engines (eg X!Tandem) can't create those subsets on the fly .. and because we need decoys embedded in the database files. With regards to cloudman ... we are definitely keen to get an instance up and running. At the moment it takes quite a bit of work to properly configure all the components to make this work well ... so a prebuilt instance would be great. Not sure if that answers your question ... but if there is something we could do to improve the integration of our tools into Galaxy I'd be happy to try it. Regards Ira On 18/04/2012, at 11:13 AM, Greg Edwards wrote:
Ira,
As part of your Proteomics Toolshed, are you thinking of making some Protein databases available ? Latest UniProt/SwissProt (~ 250 MB) or UniProt/TREMBl (~ 8GB) ? That could be very helpful for future Proteomics tools we are developing.
http://en.wikipedia.org/wiki/UniProt
Also, could it go in the Galaxy Cloudman /mnt/galaxyIndices volume ? That's a question for the Galaxy team I think.
Rgds, Greg E
On Tue, Apr 3, 2012 at 11:33 PM, Greg Von Kuster <greg@bx.psu.edu> wrote: No worries, Ira - have a great Easter vacation!
On Apr 3, 2012, at 7:20 AM, Ira Cooke wrote:
Hi Greg,
I'm afraid to say I might have been a bit ahead of myself in asking you to create that Proteomics category. We're almost ready to upload our tools, but at the last minute we've discovered a bunch of issues we need to sort out. I'm going away for Easter and won't be back until the 16th ... so I guess the earliest our tools would be up is after the 16th.
Sorry about that. I hope you're OK with a 0 beside the Proteomics category for now.
Ira
On 30/03/2012, at 10:03 AM, Ira Cooke wrote:
Thanks ... that would definitely be a good idea.
Well try to implement proper tests for all the tools.
Ira
On 30/03/2012, at 10:01 AM, Greg Von Kuster wrote:
Thanks Ira,
Just so you know, the Galaxy functional test framework now supports testing installed tools if the repository tools include tests and test datasets are included in the repository in a test-data subdirectory. Here is the relevant section of the tool shed wiki describing this:
http://wiki.g2.bx.psu.edu/Tool%20Shed#Using_Galaxy.27s_functional_test_frame...
Greg
On Mar 29, 2012, at 6:53 PM, Ira Cooke wrote:
Dear Greg,
Thanks very much for that. I'll do a last proof-read of the tools and upload later on today.
We're working on some better documentation ... to get it all working takes some extra setup steps on the part of the user.
Ira
On 30/03/2012, at 9:49 AM, Greg Von Kuster wrote:
Hello Ira,
I've added the category to the main tool shed. Thanks for the request and your upcoming contributions!
Greg Von Kuster
On Mar 29, 2012, at 5:33 PM, Ira Cooke wrote:
> Dear list, > > I would like to add a suite of proteomics tools to the toolshed but there is currently no suitable category. > > Would it be possible to add a category called Proteomics? > > Thanks > Ira
___________________________________________________________ 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:
-- Greg Edwards, Port Jackson Bioinformatics gedwards2@gmail.com
participants (3)
-
Greg Edwards -
Greg Von Kuster -
Ira Cooke