Re: [galaxy-dev] Galaxy on Cluster - how to set -a flag with username
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 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 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 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 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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>>>
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Re: [galaxy-dev] Galaxy on Cluster - how to set -a flag with username
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 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 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 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/
___
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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Re: [galaxy-dev] Galaxy on Cluster - how to set -a flag with username
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 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 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/
___
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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Re: [galaxy-dev] Galaxy on Cluster - how to set -a flag with username
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 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 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/ > ___ 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/
Re: [galaxy-dev] Galaxy on Cluster - how to set -a flag with username
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 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/
