Re: [galaxy-dev] changeset inconsistency

2012-01-20 Thread Hans-Rudolf Hotz
Hi Nate Thank you very much for your e-mail I am still testing and working on the last distribution, hopefully going live this Sunday. But I will look into downloading and upgrading (one of our dev servers) to the new distribution next week. Regards, Hans On 01/19/2012 07:39 PM, Nate

[galaxy-dev] .gz extension gets stripped off when uploading via data library Upload via filesystem paths but not via Get Data - Upload File

2012-01-20 Thread Leandro Hermida
Hello, We've created a new binary datatype for .fastq.gz files following the same methodology as the BAM files since we don't want our fasta.gz files to be gunzipped. I added the appropriate code in upload.py to make sure of this. This new datatype and extension successfully does not gunzip our

Re: [galaxy-dev] .gz extension gets stripped off when uploading via data library Upload via filesystem paths but not via Get Data - Upload File

2012-01-20 Thread Peter Cock
On Fri, Jan 20, 2012 at 12:42 PM, Leandro Hermida soft...@leandrohermida.com wrote: Hello, We've created a new binary datatype for .fastq.gz files following the same methodology as the BAM files since we don't want our fasta.gz files to be gunzipped.  I added the appropriate code in upload.py

[galaxy-dev] postgres user change problem

2012-01-20 Thread Holger Klein
Dear all, due to some work on the user management of our servers we had to rename the user galaxy runs as. Up to now we used ident as postgres authentication method, meaning that here postgres expects unix username galaxy to have permissions of galaxy postgres user. The entry in

Re: [galaxy-dev] .gz extension gets stripped off when uploading via data library Upload via filesystem paths but not via Get Data - Upload File

2012-01-20 Thread Greg Von Kuster
Hello Leandro, I believe this behavior is due to the make_library_uploaded_dataset() method in the ~/lib/galaxy/web/controllers/library_common controller. The current method looks like this: def make_library_uploaded_dataset( self, trans, cntrller, params, name, path, type,

Re: [galaxy-dev] .gz extension gets stripped off when uploading via data library Upload via filesystem paths but not via Get Data - Upload File

2012-01-20 Thread Leandro Hermida
Hi Peter, Sorry I wasn't clear, the .gz gets stripped from the name in the Galaxy UI when you upload the files into a data library via the manage data libraries form. When you upload it via Get Data - Upload File the .gz is preserved which is what one would want since I am not having it gunzipped

Re: [galaxy-dev] running functional tests on a galaxy server

2012-01-20 Thread Nate Coraor
On Jan 19, 2012, at 12:57 AM, Fields, Christopher J wrote: Just to add for the list, nate mentioned on IRC that running tests on an external server likely doesn't work at the moment but that ./scripts/functional_tests.py may have something to work with via environment variables. The tool

Re: [galaxy-dev] .gz extension gets stripped off when uploading via data library Upload via filesystem paths but not via Get Data - Upload File

2012-01-20 Thread Leandro Hermida
Hi Greg, Ok this code change to library_common.py works, now when you use the data libraries menu to bring in .fastq.gz files it doesn't cut off the .gz thank you! best, Leandro On Fri, Jan 20, 2012 at 3:32 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Leandro, I believe this behavior is

Re: [galaxy-dev] job quotas

2012-01-20 Thread Nate Coraor
On Jan 19, 2012, at 11:27 AM, Ivan Merelli wrote: Hi, is it possible to restrict the number of concurrent jobs for a single user in a local instance of galaxy? I see that in the public site this feature is implemented, but I don't find documentation about how to implement this locally. I

Re: [galaxy-dev] Status on importing BAM file into Library does not update

2012-01-20 Thread Nate Coraor
On Jan 18, 2012, at 11:54 AM, Ryan Golhar wrote: Nate - Is there a specific place in the Galaxy code that forks the samtools index on bam files on the cluster or the head node? I really need to track this down. Hey Ryan, Sorry it's taken so long, I've been pretty busy. The relevant code

[galaxy-dev] January 20, 2012 Galaxy Development News Brief

2012-01-20 Thread Jennifer Jackson
January 20, 2012 Galaxy Development News Brief Highlights: * New Object Store data integration layer introduced * RNA-seq updates: TopHat to 1.4.0 and Cufflinks, CuffDiff, CuffCompare to 1.3.0. * Tool Shed installation features and community tool additions * Trackster performance upgrades and

Re: [galaxy-dev] Status on importing BAM file into Library does not update

2012-01-20 Thread Ryan Golhar
Thanks Nate. I'll play with that. Could it be that Galaxy is trying to reset the permissions or ownership of the imported BAM files. I'm not copying them into Galaxy, rather I am linking to them. That is the only error I see in runner0.log that indicates any type of failure. On Fri, Jan 20,

Re: [galaxy-dev] Status on importing BAM file into Library does not update

2012-01-20 Thread Nate Coraor
Galaxy shouldn't be trying to do that, but it also shouldn't cause metadata to fail. On Jan 20, 2012, at 10:52 AM, Ryan Golhar wrote: Thanks Nate. I'll play with that. Could it be that Galaxy is trying to reset the permissions or ownership of the imported BAM files. I'm not copying them

[galaxy-dev] problem with Input dataset workflow control feature and custom non-subclass datatypes

2012-01-20 Thread Leandro Hermida
Hi, There seems to be a weird bug with the Input dataset workflow control feature, hard to explain clearly but I'll try my best. If you define a custom datatype that is a simple subclass of an existing galaxy datatype, e.g.: datatype extension=myext type=galaxy.datatypes.data:Text subclass=True

Re: [galaxy-dev] running functional tests on a galaxy server

2012-01-20 Thread Fields, Christopher J
Thanks Nate. I have tried that but it seems to run into problems with the expected output. This may be simply the aforementioned python dependency issues, but I'll have to investigate more in the coming week when I have time. Just to get an idea of what I would like, I mainly want the

Re: [galaxy-dev] Status on importing BAM file into Library does not update

2012-01-20 Thread Shantanu Pavgi
Just wanted to add that we have consistently seen this issue of 'samtools index' running locally on our install. We are using SGE scheduler. Thanks for pointing out details in the code Nate. -- Shantanu. On Jan 20, 2012, at 9:35 AM, Nate Coraor wrote: On Jan 18, 2012, at 11:54 AM, Ryan

Re: [galaxy-dev] Galaxy Hang after DrmCommunicationException

2012-01-20 Thread Nate Coraor
On Jan 11, 2012, at 12:18 PM, Ann Black wrote: Good Morning galaxy group! I was hoping that someone might have some ideas on a problem we have experienced a handful of times running galaxy on our local cluster. Occasionally we experience some communication timeouts between out cluster

Re: [galaxy-dev] samtools version detection issue

2012-01-20 Thread Nate Coraor
On Jan 20, 2012, at 12:12 AM, ambarish biswas wrote: Hi, I'm not sure if this is related or not but I'm also noticed a similar problem where the program is not found in the path, but it exists. I have it submitted as an issue , but it could be related here so mentioned here. The problem

Re: [galaxy-dev] Galaxy Hang after DrmCommunicationException

2012-01-20 Thread Edward Kirton
yes, nate but that fails the job but it is, in fact, still running and the error should be ignored except Exception, e: # so we don't kill the monitor thread log.exception((%s/%s) Unable to check job status % ( galaxy_job_id, job_id ) )

Re: [galaxy-dev] how to use projects for fair-share on compute-cluster

2012-01-20 Thread Edward Kirton
Great idea, Nate (hint! hint!). On Thu, Jan 19, 2012 at 10:27 AM, Nate Coraor n...@bx.psu.edu wrote: Hey Ed, This is a neat approach.  You could possibly also do this in the Galaxy database by associating users and groups with roles that match project names.  A select list or history

Re: [galaxy-dev] how to use projects for fair-share on compute-cluster

2012-01-20 Thread Glen Beane
I really want this for Torque/Moab where the native spec flag is -A Sent from my iPhone On Jan 20, 2012, at 7:34 PM, Edward Kirton eskir...@lbl.gov wrote: Great idea, Nate (hint! hint!). On Thu, Jan 19, 2012 at 10:27 AM, Nate Coraor n...@bx.psu.edu wrote: Hey Ed, This is a neat