I'm confused. Why would the symlink cause problems for Cuffcompare but not for other tools that use symlinks (including Cufflinks and Cuffdiff)?
J. On Sep 8, 2011, at 1:43 PM, Chorny, Ilya wrote: > 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.goe...@emory.edu] > Sent: Wednesday, September 07, 2011 6:26 PM > To: Chorny, Ilya > Cc: email@example.com > 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, > J. > > 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-boun...@lists.bx.psu.edu > [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya > Sent: Wednesday, September 07, 2011 9:18 AM > To: firstname.lastname@example.org > 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: icho...@illumina.com > Website: www.illumina.com > > > ___________________________________________________________ > 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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