Chorny, Ilya wrote:

Ok, so I figured out how to get the username in drama.py and pass it along to SGE(in our case) using the Gordon patch. Now I am getting an error that "Job output not returned from cluster" which comes from the finish job sub routine in drama.py . I am assuming this is because the .dat file are owned by the galaxy user and do not have write permission by other users. Where are these files created? I am hoping to add a system call to chmod to see if this fixes the problem.

The output files are created in lib/galaxy/tools/actions/*.py.

__init__.py:

# Create an empty file immediately open( data.file_name, "w" ).close()

upload_common.py:

# Create an empty file immediately if not dataset.dataset.external_filename: open( dataset.file_name, "w" ).close()

--nate

Thanks,

Ilya

-----Original Message----- From: Nate Coraor [mailto:nate@bx.psu.edu] Sent: Thursday, June 09, 2011 9:47 AM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Passing username to drmaa.py

Chorny, Ilya wrote:

...

I am trying to figure out how to pass the current user name to drama.py. I have had little success so far. None of the environmental variables contain any current user information. Any thoughts?

Thanks,

Ilya

Hi Ilya,

You can use $__user_email__ in the command template in the tool's configuration, if you need it there. In the drmaa.py code itself, you can use the '.user' property on the job wrapper to get the email address.

--nate

...

Ilya Chorny Ph.D. Bioinformatics - Intern ichorny@illumina.commailto:ichorny@illumina.com 858-202-4582

...

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Chorny, Ilya wrote:

I found the statement in __init__.py but not in upload_common.py.

Sorry, it's in a commit newer than the latest stable release.

--nate

Thanks,

Ilya

-----Original Message----- From: Nate Coraor [mailto:nate@bx.psu.edu] Sent: Wednesday, June 15, 2011 8:47 AM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Passing username to drmaa.py

Chorny, Ilya wrote:

...

Ok, so I figured out how to get the username in drama.py and pass it along to SGE(in our case) using the Gordon patch. Now I am getting an error that "Job output not returned from cluster" which comes from the finish job sub routine in drama.py . I am assuming this is because the .dat file are owned by the galaxy user and do not have write permission by other users. Where are these files created? I am hoping to add a system call to chmod to see if this fixes the problem.

The output files are created in lib/galaxy/tools/actions/*.py.

__init__.py:

# Create an empty file immediately
open( data.file_name, "w" ).close()

upload_common.py:

# Create an empty file immediately
if not dataset.dataset.external_filename:
    open( dataset.file_name, "w" ).close()

--nate

...

Thanks,

Ilya

-----Original Message----- From: Nate Coraor [mailto:nate@bx.psu.edu] Sent: Thursday, June 09, 2011 9:47 AM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Passing username to drmaa.py

Chorny, Ilya wrote:

...

I am trying to figure out how to pass the current user name to drama.py. I have had little success so far. None of the environmental variables contain any current user information. Any thoughts?

Thanks,

Ilya

Hi Ilya,

You can use $__user_email__ in the command template in the tool's configuration, if you need it there. In the drmaa.py code itself, you can use the '.user' property on the job wrapper to get the email address.

--nate

...

Ilya Chorny Ph.D. Bioinformatics - Intern ichorny@illumina.commailto:ichorny@illumina.com 858-202-4582

...

---

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/