Re: [galaxy-dev] cuffcompare wrapper

[Jeremy Goecks]

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: 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,
> 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: 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: 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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Re: [galaxy-dev] cuffcompare wrapper

[Chorny, Ilya]

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: 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,
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> 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu]<mailto:[mailto:galaxy-dev-boun...@lists.bx.psu.edu]>
 On Behalf Of Chorny, Ilya
Sent: Wednesday, September 07, 2011 9:18 AM
To: galaxy-dev@lists.bx.psu.edu<mailto: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: icho...@illumina.com<mailto:icho...@illumina.com>
Website: www.illumina.com<http://www.illumina.com/>


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Re: [galaxy-dev] cuffcompare wrapper

[Jeremy Goecks]

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: 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: 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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Re: [galaxy-dev] cuffcompare wrapper

[Chorny, Ilya]

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: 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: icho...@illumina.com<mailto:icho...@illumina.com>
Website: www.illumina.com<http://www.illumina.com>


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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/

[galaxy-dev] cuffcompare wrapper

[Chorny, Ilya]

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/