bwa_mem and "-t" option

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bwa_mem and "-t" option

David Kovalic-3
Hi,

Is it possible, and if so how, to run the galaxy devteam (version 546ada4a9f43) of bwa_mem with the "-t" option and a value >1?

"-t INT number of threads [1]"

This would be quite useful, and used, for accelerating single bwa mem jobs.

Thanks,

David


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Re: bwa_mem and "-t" option

Björn Grüning-3
Hi David,

this is possible via the GALAXY_SLOTS mechanism. An admin can give every
tool it's own environment and can set GALAXY_SLOTS dynamically.
A user can not do this, as this is highly dependent on the node this
tool will run and normally a user does not know about this.

However, if you really want to offer this to a user, Galaxy also offers
to enable this option per tool level and will add additional parameter
fields to set GALAXY_SLOTS as a user.

Cheers,
Bjoern

Am 26.05.2017 um 20:23 schrieb David Kovalic:

> Hi,
>
> Is it possible, and if so how, to run the galaxy devteam
> (version 546ada4a9f43) of bwa_mem with the "-t" option and a value >1?
>
>     "-t INT number of threads [1]"
>
>
> This would be quite useful, and used, for accelerating single bwa mem jobs.
>
> Thanks,
>
> David
>
>
>
> ___________________________________________________________
> 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/
>
___________________________________________________________
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/

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Re: bwa_mem and "-t" option

David Kovalic-3
Bjoern,

Thanks for the response.

I agree with the first approach (admin control of the per tool environment). Do you know… are there docs or similar resources you could point me to that describe how to achieve this?

Thanks again,

David



On Sun, May 28, 2017 4:41 AM, Björn Grüning [hidden email] wrote:

Hi David,


this is possible via the GALAXY_SLOTS mechanism. An admin can give every

tool it's own environment and can set GALAXY_SLOTS dynamically.

A user can not do this, as this is highly dependent on the node this

tool will run and normally a user does not know about this.


However, if you really want to offer this to a user, Galaxy also offers

to enable this option per tool level and will add additional parameter

fields to set GALAXY_SLOTS as a user.


Cheers,

Bjoern


Am 26.05.2017 um 20:23 schrieb David Kovalic:

> Hi,

>

> Is it possible, and if so how, to run the galaxy devteam

> (version 546ada4a9f43) of bwa_mem with the "-t" option and a value >1?

>

> "-t INT number of threads [1]"

>

>

> This would be quite useful, and used, for accelerating single bwa mem jobs.

>

> Thanks,

>

> David

>

>

>

> ___________________________________________________________

> 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/

>



___________________________________________________________
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/

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  http://galaxyproject.org/search/
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Re: bwa_mem and "-t" option

Björn Grüning-3
HI David,

have a look at https://galaxyproject.org/admin/config/jobs/

and this config file:

https://github.com/galaxyproject/galaxy/blob/dev/config/job_resource_params_conf.xml.sample

and here:

https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample_advanced#L791

I couldn't find more information, hope this gets you started!
Cheers,
Bjoern

Am 01.06.2017 um 20:48 schrieb David Kovalic:

> Bjoern,
>
> Thanks for the response.
>
> I agree with the first approach (admin control of the per tool
> environment). Do you know… are there docs or similar resources you could
> point me to that describe how to achieve this?
>
> Thanks again,
>
> David
>
>
>
> On Sun, May 28, 2017 4:41 AM, Björn Grüning [hidden email]
> <mailto:[hidden email]> wrote:
>
>     __
>
>     Hi David,
>
>
>     this is possible via the GALAXY_SLOTS mechanism. An admin can give every
>
>     tool it's own environment and can set GALAXY_SLOTS dynamically.
>
>     A user can not do this, as this is highly dependent on the node this
>
>     tool will run and normally a user does not know about this.
>
>
>     However, if you really want to offer this to a user, Galaxy also offers
>
>     to enable this option per tool level and will add additional parameter
>
>     fields to set GALAXY_SLOTS as a user.
>
>
>     Cheers,
>
>     Bjoern
>
>
>     Am 26.05.2017 um 20:23 schrieb David Kovalic:
>
>     > Hi,
>
>     >
>
>     > Is it possible, and if so how, to run the galaxy devteam
>
>     > (version 546ada4a9f43) of bwa_mem with the "-t" option and a value >1?
>
>     >
>
>     > "-t INT number of threads [1]"
>
>     >
>
>     >
>
>     > This would be quite useful, and used, for accelerating single bwa
>     mem jobs.
>
>     >
>
>     > Thanks,
>
>     >
>
>     > David
>
>     >
>
>     >
>
>     >
>
>     > ___________________________________________________________
>
>     > 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/
>
>     >
>
>
___________________________________________________________
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/
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Re: bwa_mem and "-t" option

David Kovalic-3
Bjoern,

Thanks so much, I'll check it out. 

If I can't figure this out I am sure I can ask around in Montpellier at GCC'17! I am looking forward to the meeting and being able to visit Montpellier for the first time ever 

The help is greatly appreciated.

David



On Thu, Jun 1, 2017 2:21 PM, Björn Grüning [hidden email] wrote:

HI David,


have a look at https://galaxyproject.org/admin/config/jobs/


and this config file:


https://github.com/galaxyproject/galaxy/blob/dev/config/job_resource_params_conf.xml.sample


and here:


https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample_advanced#L791


I couldn't find more information, hope this gets you started!

Cheers,

Bjoern


Am 01.06.2017 um 20:48 schrieb David Kovalic:

> Bjoern,

>

> Thanks for the response.

>

> I agree with the first approach (admin control of the per tool

> environment). Do you know… are there docs or similar resources you could

> point me to that describe how to achieve this?

>

> Thanks again,

>

> David

>

>

>

> On Sun, May 28, 2017 4:41 AM, Björn Grüning [hidden email]

> <mailto:[hidden email]> wrote:

>

> __

>

> Hi David,

>

>

> this is possible via the GALAXY_SLOTS mechanism. An admin can give every

>

> tool it's own environment and can set GALAXY_SLOTS dynamically.

>

> A user can not do this, as this is highly dependent on the node this

>

> tool will run and normally a user does not know about this.

>

>

> However, if you really want to offer this to a user, Galaxy also offers

>

> to enable this option per tool level and will add additional parameter

>

> fields to set GALAXY_SLOTS as a user.

>

>

> Cheers,

>

> Bjoern

>

>

> Am 26.05.2017 um 20:23 schrieb David Kovalic:

>

> > Hi,

>

> >

>

> > Is it possible, and if so how, to run the galaxy devteam

>

> > (version 546ada4a9f43) of bwa_mem with the "-t" option and a value >1?

>

> >

>

> > "-t INT number of threads [1]"

>

> >

>

> >

>

> > This would be quite useful, and used, for accelerating single bwa

> mem jobs.

>

> >

>

> > Thanks,

>

> >

>

> > David

>

> >

>

> >

>

> >

>

> > ___________________________________________________________

>

> > 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/

>

> >

>

>



___________________________________________________________
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/
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Re: bwa_mem and "-t" option

Björn Grüning-3
Your are joining GCC? Cool!

Looking forward to see you there!
Bjoern

Am 01.06.2017 um 21:25 schrieb David Kovalic:

> Bjoern,
>
> Thanks so much, I'll check it out.
>
> If I can't figure this out I am sure I can ask around in Montpellier at
> GCC'17! I am looking forward to the meeting and being able to visit
> Montpellier for the first time ever
>
> The help is greatly appreciated.
>
> David
>
>
>
> On Thu, Jun 1, 2017 2:21 PM, Björn Grüning [hidden email]
> <mailto:[hidden email]> wrote:
>
>     __
>
>     HI David,
>
>
>     have a look at https://galaxyproject.org/admin/config/jobs/
>
>
>     and this config file:
>
>
>     https://github.com/galaxyproject/galaxy/blob/dev/config/job_resource_params_conf.xml.sample
>
>
>     and here:
>
>
>     https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample_advanced#L791
>
>
>     I couldn't find more information, hope this gets you started!
>
>     Cheers,
>
>     Bjoern
>
>
>     Am 01.06.2017 um 20:48 schrieb David Kovalic:
>
>     > Bjoern,
>
>     >
>
>     > Thanks for the response.
>
>     >
>
>     > I agree with the first approach (admin control of the per tool
>
>     > environment). Do you know… are there docs or similar resources you
>     could
>
>     > point me to that describe how to achieve this?
>
>     >
>
>     > Thanks again,
>
>     >
>
>     > David
>
>     >
>
>     >
>
>     >
>
>     > On Sun, May 28, 2017 4:41 AM, Björn Grüning [hidden email]
>
>     > <mailto:[hidden email]> wrote:
>
>     >
>
>     > __
>
>     >
>
>     > Hi David,
>
>     >
>
>     >
>
>     > this is possible via the GALAXY_SLOTS mechanism. An admin can give
>     every
>
>     >
>
>     > tool it's own environment and can set GALAXY_SLOTS dynamically.
>
>     >
>
>     > A user can not do this, as this is highly dependent on the node this
>
>     >
>
>     > tool will run and normally a user does not know about this.
>
>     >
>
>     >
>
>     > However, if you really want to offer this to a user, Galaxy also
>     offers
>
>     >
>
>     > to enable this option per tool level and will add additional parameter
>
>     >
>
>     > fields to set GALAXY_SLOTS as a user.
>
>     >
>
>     >
>
>     > Cheers,
>
>     >
>
>     > Bjoern
>
>     >
>
>     >
>
>     > Am 26.05.2017 um 20:23 schrieb David Kovalic:
>
>     >
>
>     > > Hi,
>
>     >
>
>     > >
>
>     >
>
>     > > Is it possible, and if so how, to run the galaxy devteam
>
>     >
>
>     > > (version 546ada4a9f43) of bwa_mem with the "-t" option and a
>     value >1?
>
>     >
>
>     > >
>
>     >
>
>     > > "-t INT number of threads [1]"
>
>     >
>
>     > >
>
>     >
>
>     > >
>
>     >
>
>     > > This would be quite useful, and used, for accelerating single bwa
>
>     > mem jobs.
>
>     >
>
>     > >
>
>     >
>
>     > > Thanks,
>
>     >
>
>     > >
>
>     >
>
>     > > David
>
>     >
>
>     > >
>
>     >
>
>     > >
>
>     >
>
>     > >
>
>     >
>
>     > > ___________________________________________________________
>
>     >
>
>     > > 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/
>
>     >
>
>     > >
>
>     >
>
>     >
>
>
___________________________________________________________
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/
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