Re: [galaxy-dev] Is dynamic associated information per dataset possible?

[Ross]

> Duddy, John wrote:
>> The sample tracking system looks interesting. It looks like this is designed 
>> to have the sequencers modeled in Galaxy, have Galaxy pull the data from the 
>> sequencers, and might assume 1-1 pairing between sequencing run and samples.
>> I'd like to be able to support pushing files from a central location and 
>> variably multiplexed runs, all via the API (or extensions to the API).Is 
>> there any up-to-date documentation on this feature?
> The sample tracking system is undergoing a bunch of changes, so I'm
> thinking the documentation will be rewritten after that.

There's some code from Brad Chapman at
https://github.com/chapmanb/bcbb/tree/master/nextgen/scripts that
specifically addresses some of your downstream use cases and more.
Currently involves deep galaxy introspection into the sequencing
system. As Nate said, that's undergoing replumbing, so that interface
part will need changes - but the rest is likely a great starting point
for putting together your own local common tasks like (eg) splitting
and analysing a multiplexed lane and calling variants and other
routine core lab kinds of operations.
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Re: [galaxy-dev] Is dynamic associated information per dataset possible?

[Nate Coraor]

Duddy, John wrote:
> That's good news. Is this available via the API as well? I didn't see 
> examples of this anywhere in the code, but I thought it might be available by 
> passing additional values in the dictionary.

I don't think it has been done, but as you say, it may be possible just
via an arg in the dictionary.

--nate

> 
> 
> -Original Message-
> From: Nate Coraor [mailto:n...@bx.psu.edu] 
> Sent: Thursday, May 26, 2011 1:38 AM
> To: Duddy, John
> Cc: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] Is dynamic associated information per dataset 
> possible?
> 
> Duddy, John wrote:
> > We'd like to be able to associate fixed things (project, Sample, sequencer 
> > used) with user's FASTQ files, and we'd also like to allow users to 
> > associate dynamic, site-specific stuff with the sequencing run. Currently, 
> > users track their runs using a CSV sample sheet, and often they add columns 
> > to that sample sheet for their own information.
> > 
> > Is it possible to associate that information with the FASTQ file when it is 
> > placed in Galaxy? I know about metadata, but the supported fields look like 
> > they are fixed in the code. I was hoping for a solution where the users do 
> > not need to modify the Galaxy code to pull this off.
> 
> Hi John,
> 
> You could accomplish this with library templates:
> 
> https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/LibraryTemplates
> 
> --nate
> 
> > 
> > John Duddy
> > Sr. Staff Software Engineer
> > Illumina, Inc.
> > 9885 Towne Centre Drive
> > San Diego, CA 92121
> > Tel: 858-736-3584
> > E-mail: jdu...@illumina.com<mailto:jdu...@illumina.com>
> > 
> 
> > ___
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> > and other Galaxy lists, please use the interface at:
> > 
> >   http://lists.bx.psu.edu/
> 
> 
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Re: [galaxy-dev] Is dynamic associated information per dataset possible?

[Nate Coraor]

Duddy, John wrote:
> The sample tracking system looks interesting. It looks like this is designed 
> to have the sequencers modeled in Galaxy, have Galaxy pull the data from the 
> sequencers, and might assume 1-1 pairing between sequencing run and samples. 
> 
> I'd like to be able to support pushing files from a central location and 
> variably multiplexed runs, all via the API (or extensions to the API).
> 
> Is there any up-to-date documentation on this feature?

The sample tracking system is undergoing a bunch of changes, so I'm
thinking the documentation will be rewritten after that.

--nate

> 
> John Duddy
> Sr. Staff Software Engineer
> Illumina, Inc.
> 9885 Towne Centre Drive
> San Diego, CA 92121
> Tel: 858-736-3584
> E-mail: jdu...@illumina.com
> 
> 
> -Original Message-
> From: Greg Von Kuster [mailto:g...@bx.psu.edu] 
> Sent: Thursday, May 26, 2011 2:18 AM
> To: Duddy, John
> Cc: galaxy-dev
> Subject: Re: [galaxy-dev] Is dynamic associated information per dataset 
> possible?
> 
> In addition to Data Library templates, which are useful after the sequencer 
> data has arrived in a Galaxy Data Library, Galaxy's sample tracking system 
> includes sample run templates which are very similar to the Data Library 
> templates, but are associated with a sample as it progresses through it's 
> sequence run lifecycle in the facility.  Sample run details templates are 
> defined by the facility administrator.  They can be created in the Admin view 
> via the Manage form definitions menu link.
> 
> 
> 
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Re: [galaxy-dev] Is dynamic associated information per dataset possible?

[Duddy, John]

The sample tracking system looks interesting. It looks like this is designed to 
have the sequencers modeled in Galaxy, have Galaxy pull the data from the 
sequencers, and might assume 1-1 pairing between sequencing run and samples. 

I'd like to be able to support pushing files from a central location and 
variably multiplexed runs, all via the API (or extensions to the API).

Is there any up-to-date documentation on this feature?

John Duddy
Sr. Staff Software Engineer
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Tel: 858-736-3584
E-mail: jdu...@illumina.com


-Original Message-
From: Greg Von Kuster [mailto:g...@bx.psu.edu] 
Sent: Thursday, May 26, 2011 2:18 AM
To: Duddy, John
Cc: galaxy-dev
Subject: Re: [galaxy-dev] Is dynamic associated information per dataset 
possible?

In addition to Data Library templates, which are useful after the sequencer 
data has arrived in a Galaxy Data Library, Galaxy's sample tracking system 
includes sample run templates which are very similar to the Data Library 
templates, but are associated with a sample as it progresses through it's 
sequence run lifecycle in the facility.  Sample run details templates are 
defined by the facility administrator.  They can be created in the Admin view 
via the Manage form definitions menu link.



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Re: [galaxy-dev] Is dynamic associated information per dataset possible?

[Duddy, John]

That's good news. Is this available via the API as well? I didn't see examples 
of this anywhere in the code, but I thought it might be available by passing 
additional values in the dictionary.


-Original Message-
From: Nate Coraor [mailto:n...@bx.psu.edu] 
Sent: Thursday, May 26, 2011 1:38 AM
To: Duddy, John
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Is dynamic associated information per dataset 
possible?

Duddy, John wrote:
> We'd like to be able to associate fixed things (project, Sample, sequencer 
> used) with user's FASTQ files, and we'd also like to allow users to associate 
> dynamic, site-specific stuff with the sequencing run. Currently, users track 
> their runs using a CSV sample sheet, and often they add columns to that 
> sample sheet for their own information.
> 
> Is it possible to associate that information with the FASTQ file when it is 
> placed in Galaxy? I know about metadata, but the supported fields look like 
> they are fixed in the code. I was hoping for a solution where the users do 
> not need to modify the Galaxy code to pull this off.

Hi John,

You could accomplish this with library templates:

https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/LibraryTemplates

--nate

> 
> John Duddy
> Sr. Staff Software Engineer
> Illumina, Inc.
> 9885 Towne Centre Drive
> San Diego, CA 92121
> Tel: 858-736-3584
> E-mail: jdu...@illumina.com<mailto:jdu...@illumina.com>
> 

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Re: [galaxy-dev] Is dynamic associated information per dataset possible?

[Nate Coraor]

Roman Valls wrote:
> Nate, is it just me or all the .png links on that wikipage are
> broken/missing ? :-S

Hi Roman,

We've had occasional problems with the images in the wiki, and I think
sometimes they'll show up, sometimes they won't.  We're in the process
of migrating the wiki to our own Moin install, so this should be fixed
then.

--nate

> 
> On 2011-05-26 10:38, Nate Coraor wrote:
> > Duddy, John wrote:
> >> We'd like to be able to associate fixed things (project, Sample, sequencer 
> >> used) with user's FASTQ files, and we'd also like to allow users to 
> >> associate dynamic, site-specific stuff with the sequencing run. Currently, 
> >> users track their runs using a CSV sample sheet, and often they add 
> >> columns to that sample sheet for their own information.
> >>
> >> Is it possible to associate that information with the FASTQ file when it 
> >> is placed in Galaxy? I know about metadata, but the supported fields look 
> >> like they are fixed in the code. I was hoping for a solution where the 
> >> users do not need to modify the Galaxy code to pull this off.
> > 
> > Hi John,
> > 
> > You could accomplish this with library templates:
> > 
> > https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/LibraryTemplates
> > 
> > --nate
> > 
> >>
> >> John Duddy
> >> Sr. Staff Software Engineer
> >> Illumina, Inc.
> >> 9885 Towne Centre Drive
> >> San Diego, CA 92121
> >> Tel: 858-736-3584
> >> E-mail: jdu...@illumina.com
> >>
> > 
> >> ___
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> >> in your mail client.  To manage your subscriptions to this
> >> and other Galaxy lists, please use the interface at:
> >>
> >>   http://lists.bx.psu.edu/
> > 
> > ___
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Re: [galaxy-dev] Is dynamic associated information per dataset possible?

[Peter Cock]

On Thu, May 26, 2011 at 10:34 AM, Roman Valls  wrote:
> Nate, is it just me or all the .png links on that wikipage are
> broken/missing ? :-S

I've noticed this on other pages, I think some stuff got moved a while back.
They just need the folder name prefixed...

Peter
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Re: [galaxy-dev] Is dynamic associated information per dataset possible?

[Roman Valls]

Nate, is it just me or all the .png links on that wikipage are
broken/missing ? :-S

On 2011-05-26 10:38, Nate Coraor wrote:
> Duddy, John wrote:
>> We'd like to be able to associate fixed things (project, Sample, sequencer 
>> used) with user's FASTQ files, and we'd also like to allow users to 
>> associate dynamic, site-specific stuff with the sequencing run. Currently, 
>> users track their runs using a CSV sample sheet, and often they add columns 
>> to that sample sheet for their own information.
>>
>> Is it possible to associate that information with the FASTQ file when it is 
>> placed in Galaxy? I know about metadata, but the supported fields look like 
>> they are fixed in the code. I was hoping for a solution where the users do 
>> not need to modify the Galaxy code to pull this off.
> 
> Hi John,
> 
> You could accomplish this with library templates:
> 
> https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/LibraryTemplates
> 
> --nate
> 
>>
>> John Duddy
>> Sr. Staff Software Engineer
>> Illumina, Inc.
>> 9885 Towne Centre Drive
>> San Diego, CA 92121
>> Tel: 858-736-3584
>> E-mail: jdu...@illumina.com
>>
> 
>> ___
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>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>
>>   http://lists.bx.psu.edu/
> 
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Re: [galaxy-dev] Is dynamic associated information per dataset possible?

[Nate Coraor]

Duddy, John wrote:
> We'd like to be able to associate fixed things (project, Sample, sequencer 
> used) with user's FASTQ files, and we'd also like to allow users to associate 
> dynamic, site-specific stuff with the sequencing run. Currently, users track 
> their runs using a CSV sample sheet, and often they add columns to that 
> sample sheet for their own information.
> 
> Is it possible to associate that information with the FASTQ file when it is 
> placed in Galaxy? I know about metadata, but the supported fields look like 
> they are fixed in the code. I was hoping for a solution where the users do 
> not need to modify the Galaxy code to pull this off.

Hi John,

You could accomplish this with library templates:

https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/LibraryTemplates

--nate

> 
> John Duddy
> Sr. Staff Software Engineer
> Illumina, Inc.
> 9885 Towne Centre Drive
> San Diego, CA 92121
> Tel: 858-736-3584
> E-mail: jdu...@illumina.com
> 

> ___
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[galaxy-dev] Is dynamic associated information per dataset possible?

[Duddy, John]

We'd like to be able to associate fixed things (project, Sample, sequencer 
used) with user's FASTQ files, and we'd also like to allow users to associate 
dynamic, site-specific stuff with the sequencing run. Currently, users track 
their runs using a CSV sample sheet, and often they add columns to that sample 
sheet for their own information.

Is it possible to associate that information with the FASTQ file when it is 
placed in Galaxy? I know about metadata, but the supported fields look like 
they are fixed in the code. I was hoping for a solution where the users do not 
need to modify the Galaxy code to pull this off.

John Duddy
Sr. Staff Software Engineer
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Tel: 858-736-3584
E-mail: jdu...@illumina.com

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