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 margeemail@gmail.com 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

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 margeemail@gmail.com 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 margeemail@gmail.com 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/

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 margeemail@gmail.com 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 chilton@msi.umn.edu 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 margeemail@gmail.com 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 margeemail@gmail.com 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/