Thanks Nate! I set 'debug = False'and now I have no problem downloading my BAM/SAM files.

Cheers, Liisa

From: Nate Coraor nate@bx.psu.edu To: Liisa Koski liisa.koski@dnalandmarks.ca Cc: galaxy-dev@bx.psu.edu Date: 2011-03-22 12:06 Subject: Re: [galaxy-dev] Can't save BAM file from Galaxy

Liisa Koski wrote:

Hello, I have a local instance of galaxy and after successfully running an NGS analysis I am trying to save my BAM file to my local machine. When I

click

on the save icon my Galaxy instance crashes with the following error.

This

also happens when I try to save the SAM file. It does not happen when I try to save a txt file.

python: ./Modules/cStringIO.c:419: O_cwrite: Assertion `oself->pos + l <

2147483647' failed. ./run.sh: line 48: 19187 Aborted python ./scripts/paster.py serve universe_wsgi.ini $@

Something to do with base positions?

Hi Liisa,

I'm not completely certain, but it may just be the debugging modules that are enabled by default trying to load the entire bam/sam file into memory before sending it. Try restarting your Galaxy server after setting 'debug = False' in universe_wsgi.ini and see if this makes a difference.

--nate

Thanks in advance for any help, Liisa

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Ryan Golhar wrote:

Nate - Is there a way to get the pbs job scripts to still get saved with debugging turned off? I'm running into this same problem but still prefer to have the job scripts kept in case something goes wrong.

Not without modifying the call to cleanup() in the job runner (lib/galaxy/jobs/__init__.py). It'd be a simple change, though.

Ryan

Assaf Gordon wrote:

+1

Nate Coraor wrote, On 03/31/2011 12:34 PM:

...

Ryan Golhar wrote:

...

Nate - Is there a way to get the pbs job scripts to still get saved with debugging turned off?

Not without modifying the call to cleanup() in the job runner (lib/galaxy/jobs/__init__.py). It'd be a simple change, though.

It would be beneficial if instead of one generic "debug=true" there would be separate debug statement in the INI for each module or feature.

I go back and forth on this stuff, since we also run the risk of having so many options in the config file that it begins to become unmanageable. If this would be a useful one to break out it can certainly be done.

--nate

Just a thought, -gordon ___________________________________________________________ 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:

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