It’s not an issue in the tmp dir but in the job_working_directory. I run most of those other tools with no problems. I don’t think we should make it a requirement across the board and I think we can come up with alternative ways to clean up the job_working_directory. I am hoping that you could add the symlink to the cuffcompare wrapper as it is the only one where the symlink causes me a problem as far as I have tested. We don’t want to have our code base differ to much from galaxy-central.

Thanks,

Ilya

From: Jeremy Goecks [mailto:jeremy.goecks@emory.edu]
Sent: Wednesday, September 07, 2011 6:26 PM
To: Chorny, Ilya
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] cuffcompare wrapper

Ilya,

A search of the Galaxy codebase indicates that thirteen tools use symlinks (e.g. GATK, Sicer, Picard, Cuff*, Bowtie), so the changes required to support this new code are significant. (Changes would also likely be needed for tools in the tool shed.) Also, asking tool wrappers to delete symlinks would be an idiosyncratic requirement as tools assume they have a temporary working directory at their disposal.

For these reasons, it seems best to have the tool framework clean up symlinks as necessary to support the new code.

Best,

On Sep 7, 2011, at 2:28 PM, Chorny, Ilya wrote:

Ok, I figured out why you need the symlink.

Can you add an unlink after the process completes?

i.e

for i, arg in enumerate( args ):

input_file_name = "./input%i" % ( i+1 )

os.unlink(input_file_name)

From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Chorny, Ilya
Sent: Wednesday, September 07, 2011 9:18 AM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] cuffcompare wrapper

Hi Jeremy,

The symlink in the cuffcompare wrapper was causing galaxy to crash because I run as the actual user and have to chmod the job_working directory at the end so Galaxy can clean it up. Turns out is seems like the symlink is not needed. Am I missing something. See below.

Your code:

for i, arg in enumerate( args ):

input_file_name = "./input%i" % ( i+1 )

os.symlink( arg, input_file_name )

cmd += "%s " % input_file_name

My code:

for i, arg in enumerate( args ):

cmd += arg

Ilya Chorny Ph.D.

Bioinformatics Scientist I

Illumina, Inc.

9885 Towne Centre Drive

San Diego, CA 92121

Work: 858.202.4582

Email: ichorny@illumina.com

Website: www.illumina.com

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