Galaxy on Cluster - how to set -a flag with username

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Galaxy on Cluster - how to set -a flag with username

greg-2
In our local galaxy install we want the cluster jobs to be run from
the galaxy user but we want to include a -a [account name] to our grid
software bills properly.

Here's what I currently have in universe.wsgi:

default_cluster_job_runner = drmaa://-V -pe batch 8/

What I want is something like this:

default_cluster_job_runner = drmaa://-V -pe batch 8 -a [logged in user name]/

Is this possible?

Thanks,

Greg
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Re: Galaxy on Cluster - how to set -a flag with username

greg-2
Hi guys,

I just wanted to check in and see if anyone had any ideas on this.
(It's actually the -A flag I'm after.)

I did try putting this in universe.wsgi:

default_cluster_job_runner = drmaa://-V -pe batch 8 -A Account_Name/

I was thinking galaxy might substitute the user name for
"Account_Name" but no luck :-(

-Greg

On Tue, Mar 12, 2013 at 1:42 PM, greg <[hidden email]> wrote:

> In our local galaxy install we want the cluster jobs to be run from
> the galaxy user but we want to include a -a [account name] to our grid
> software bills properly.
>
> Here's what I currently have in universe.wsgi:
>
> default_cluster_job_runner = drmaa://-V -pe batch 8/
>
> What I want is something like this:
>
> default_cluster_job_runner = drmaa://-V -pe batch 8 -a [logged in user name]/
>
> Is this possible?
>
> Thanks,
>
> Greg
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Re: Galaxy on Cluster - how to set -a flag with username

James Taylor
Greg, I don't think there is currently any support for variable substitution of this sort in job runner configuration, but it could definitely be added. Worth filing as an issue. 


--
James Taylor, Assistant Professor, Biology/CS, Emory University


On Wed, Mar 13, 2013 at 8:12 AM, greg <[hidden email]> wrote:
Hi guys,

I just wanted to check in and see if anyone had any ideas on this.
(It's actually the -A flag I'm after.)

I did try putting this in universe.wsgi:

default_cluster_job_runner = drmaa://-V -pe batch 8 -A Account_Name/

I was thinking galaxy might substitute the user name for
"Account_Name" but no luck :-(

-Greg

On Tue, Mar 12, 2013 at 1:42 PM, greg <[hidden email]> wrote:
> In our local galaxy install we want the cluster jobs to be run from
> the galaxy user but we want to include a -a [account name] to our grid
> software bills properly.
>
> Here's what I currently have in universe.wsgi:
>
> default_cluster_job_runner = drmaa://-V -pe batch 8/
>
> What I want is something like this:
>
> default_cluster_job_runner = drmaa://-V -pe batch 8 -a [logged in user name]/
>
> Is this possible?
>
> Thanks,
>
> Greg
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and other Galaxy lists, please use the interface at:

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Re: Galaxy on Cluster - how to set -a flag with username

John Chilton
In reply to this post by greg-2
Greg,

I think you can do this with dynamic job runners.

http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010080.html

Step 1) Set:

default_cluster_job_runner = dynamic:///python/default_runner

Step 2) Create the file `lib/galaxy/jobs/rules/200_runners.py`, with
contents something like this:

def default_runner(user_email):
     username = user_email.split("@")[0]
     return "drmaa://-V -pe batch 8 -A %s/" % username

and you should be good to go.

-John



On Wed, Mar 13, 2013 at 7:12 AM, greg <[hidden email]> wrote:

> Hi guys,
>
> I just wanted to check in and see if anyone had any ideas on this.
> (It's actually the -A flag I'm after.)
>
> I did try putting this in universe.wsgi:
>
> default_cluster_job_runner = drmaa://-V -pe batch 8 -A Account_Name/
>
> I was thinking galaxy might substitute the user name for
> "Account_Name" but no luck :-(
>
> -Greg
>
> On Tue, Mar 12, 2013 at 1:42 PM, greg <[hidden email]> wrote:
>> In our local galaxy install we want the cluster jobs to be run from
>> the galaxy user but we want to include a -a [account name] to our grid
>> software bills properly.
>>
>> Here's what I currently have in universe.wsgi:
>>
>> default_cluster_job_runner = drmaa://-V -pe batch 8/
>>
>> What I want is something like this:
>>
>> default_cluster_job_runner = drmaa://-V -pe batch 8 -a [logged in user name]/
>>
>> Is this possible?
>>
>> Thanks,
>>
>> Greg
> ___________________________________________________________
> 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:
>
>   http://lists.bx.psu.edu/
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Re: Galaxy on Cluster - how to set -a flag with username

greg-2
Thanks John!  I'll give it a try.  I can't get to that link, it says
"forbidden".  Do you have another way to access the content?

What is the significance of the name 200_runners.py?

Thanks!

-Greg

On Thu, Mar 14, 2013 at 12:43 PM, John Chilton <[hidden email]> wrote:

> Greg,
>
> I think you can do this with dynamic job runners.
>
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010080.html
>
> Step 1) Set:
>
> default_cluster_job_runner = dynamic:///python/default_runner
>
> Step 2) Create the file `lib/galaxy/jobs/rules/200_runners.py`, with
> contents something like this:
>
> def default_runner(user_email):
>      username = user_email.split("@")[0]
>      return "drmaa://-V -pe batch 8 -A %s/" % username
>
> and you should be good to go.
>
> -John
>
>
>
> On Wed, Mar 13, 2013 at 7:12 AM, greg <[hidden email]> wrote:
>> Hi guys,
>>
>> I just wanted to check in and see if anyone had any ideas on this.
>> (It's actually the -A flag I'm after.)
>>
>> I did try putting this in universe.wsgi:
>>
>> default_cluster_job_runner = drmaa://-V -pe batch 8 -A Account_Name/
>>
>> I was thinking galaxy might substitute the user name for
>> "Account_Name" but no luck :-(
>>
>> -Greg
>>
>> On Tue, Mar 12, 2013 at 1:42 PM, greg <[hidden email]> wrote:
>>> In our local galaxy install we want the cluster jobs to be run from
>>> the galaxy user but we want to include a -a [account name] to our grid
>>> software bills properly.
>>>
>>> Here's what I currently have in universe.wsgi:
>>>
>>> default_cluster_job_runner = drmaa://-V -pe batch 8/
>>>
>>> What I want is something like this:
>>>
>>> default_cluster_job_runner = drmaa://-V -pe batch 8 -a [logged in user name]/
>>>
>>> Is this possible?
>>>
>>> Thanks,
>>>
>>> Greg
>> ___________________________________________________________
>> 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:
>>
>>   http://lists.bx.psu.edu/
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Re: Galaxy on Cluster - how to set -a flag with username

greg-2
Hi guys,

I got this working for a while, I have this in
/misc/local/galaxy/galaxy-dist/lib/galaxy/jobs/rules/200_runners.py:

def default_runner(user_email):
    username = user_email.split("@")[0]
    return "drmaa://-V -pe batch 8 -A %s/" % username

But lately user_email has started being passed in as None.

Any ideas what might be causing that?  Nothing has changed that I know of.

Thanks,

Greg


On Thu, Mar 21, 2013 at 3:31 PM, greg <[hidden email]> wrote:

> Thanks John!  I'll give it a try.  I can't get to that link, it says
> "forbidden".  Do you have another way to access the content?
>
> What is the significance of the name 200_runners.py?
>
> Thanks!
>
> -Greg
>
> On Thu, Mar 14, 2013 at 12:43 PM, John Chilton <[hidden email]> wrote:
>> Greg,
>>
>> I think you can do this with dynamic job runners.
>>
>> http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010080.html
>>
>> Step 1) Set:
>>
>> default_cluster_job_runner = dynamic:///python/default_runner
>>
>> Step 2) Create the file `lib/galaxy/jobs/rules/200_runners.py`, with
>> contents something like this:
>>
>> def default_runner(user_email):
>>      username = user_email.split("@")[0]
>>      return "drmaa://-V -pe batch 8 -A %s/" % username
>>
>> and you should be good to go.
>>
>> -John
>>
>>
>>
>> On Wed, Mar 13, 2013 at 7:12 AM, greg <[hidden email]> wrote:
>>> Hi guys,
>>>
>>> I just wanted to check in and see if anyone had any ideas on this.
>>> (It's actually the -A flag I'm after.)
>>>
>>> I did try putting this in universe.wsgi:
>>>
>>> default_cluster_job_runner = drmaa://-V -pe batch 8 -A Account_Name/
>>>
>>> I was thinking galaxy might substitute the user name for
>>> "Account_Name" but no luck :-(
>>>
>>> -Greg
>>>
>>> On Tue, Mar 12, 2013 at 1:42 PM, greg <[hidden email]> wrote:
>>>> In our local galaxy install we want the cluster jobs to be run from
>>>> the galaxy user but we want to include a -a [account name] to our grid
>>>> software bills properly.
>>>>
>>>> Here's what I currently have in universe.wsgi:
>>>>
>>>> default_cluster_job_runner = drmaa://-V -pe batch 8/
>>>>
>>>> What I want is something like this:
>>>>
>>>> default_cluster_job_runner = drmaa://-V -pe batch 8 -a [logged in user name]/
>>>>
>>>> Is this possible?
>>>>
>>>> Thanks,
>>>>
>>>> Greg
>>> ___________________________________________________________
>>> 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:
>>>
>>>   http://lists.bx.psu.edu/
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