Re: [galaxy-dev] Local Galaxy Instance MarkupSafe error

2011-11-03 Thread Mickael ESCUDERO
Hi Nate, It must be the issue here, I just learnt the head node is running with redhat 5 while Galaxy and all the dependencies are running on a redhat 6 server so yes the python version is not the same. I'll see what I can do with my IS department then. Cheers for the help :) Micka On 2

[galaxy-dev] GeneTrack-Installation - Version?

2011-11-03 Thread Stefanie Ververs
Hi, I sent this message about two weeks ago, but by now there was no response. I try again, maybe now someone who's got some advice notices :-) Regards, Steffi Original Message Subject:GeneTrack-Installation - Version? Date: Thu, 20 Oct 2011 23:21:25 +0200 From:

[galaxy-dev] Toolshed not showing up

2011-11-03 Thread jjv5
Hello, I am getting a strange error in attempting to use the main Galaxy toolshed. I am using the latest version: galaxy@monolith:~/galaxy-dist$ hg pull -u -r 338ead4737ba pulling from https://bitbucket.org/galaxy/galaxy-dist/ searching for changes no changes found

[galaxy-dev] Best documentation for parallel cluster support in Galaxy

2011-11-03 Thread Arthur Goldberg
Hi Where's the best documentation for parallel cluster support in Galaxy, please? BR A -- Senior Research Scientist Computational Biology Memorial Sloan-Kettering Cancer Center cBio Cancer Genomics Portal http://www.cbioportal.org/ ___

Re: [galaxy-dev] ImportError: No module named galaxy

2011-11-03 Thread Oren Livne
Dear Nate, My PYTHONPATH is already set to this value. Best, Oren ___ 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:

Re: [galaxy-dev] galaxy citation_url setting

2011-11-03 Thread Nate Coraor
Shantanu Pavgi wrote: On Nov 2, 2011, at 3:39 PM, Nate Coraor wrote: Shantanu Pavgi wrote: Hi, It seems like modification of 'citation_url' in the universe_wsgi.ini config file has no effect in the UI (Help -- How to Cite Galaxy). Is it something hard-coded in the source?

Re: [galaxy-dev] Clusters, Runners, and user credentials

2011-11-03 Thread Fields, Christopher J
Ilya, Nate, To add a bit of background to the below, we have several clusters on campus that use very different accounting systems; some run as a regular cron job to process job run info, however others use a qsub wrapper to check service units prior to job submission (a byproduct of being

Re: [galaxy-dev] Clusters, Runners, and user credentials

2011-11-03 Thread Nate Coraor
Hi Chris, Ilya's solution uses sudo to submit the job via drmaa after switching to the actual user's uid and gid. This means giving your Galaxy user sudo rights to run 3 scripts as root: * A script to submit jobs * A script to kill jobs * A script to chown a directory This could be

[galaxy-dev] Installing Galaxy on local server

2011-11-03 Thread Toqa Manasrah
Hello, I am a graduate student at GSU. I am looking for installing GALAXY on our local server http://alla.cs.gsu.edu/~software. as a result I like my server homepage start with the GALAXY interface, like this one: http://rna1.engr.uconn.edu:7474/ . after that I wish to integrate some

[galaxy-dev] Installing Galaxy on local server

2011-11-03 Thread Toqa Manasrah
Hello, I am a graduate student at GSU. I am looking for installing GALAXY on our local server http://alla.cs.gsu.edu/~software. as a result I like my server homepage start with the GALAXY interface, like this one: http://rna1.engr.uconn.edu:7474/ . after that I wish to integrate some

[galaxy-dev] Error on local galaxy using SAM-to-BAM tool on a cluster

2011-11-03 Thread Carlos Borroto
Hi, I'm running into this error: Error sorting alignments from (/tmp/5800600.1.all.q/tmpXOc5mD/tmpAZCzt_), When using SAM-to-BAM tool on a locally install Galaxy using a SGE cluster. I'm using the last version of galaxy-dist. I'm guessing I have a problem with the configuration for the tmp

Re: [galaxy-dev] Looks like actual user breaks splitting

2011-11-03 Thread Nate Coraor (n...@bx.psu.edu)
Hi John, It looks like the first issue is related to the change from get_output_fnames() - compute_outputs(). When outputs_to_working_directory = False (default) this method stores/returns a HistoryDatasetAssociation, but when True, stores/returns a Dataset (the original method's behavior).

[galaxy-dev] fastx reverse compliment failed - gzip: stdout: Broken pipe

2011-11-03 Thread Lucinda Lawson
I'm reposting over here from the user side, since this is a local instance, and it was recommended. Hi all, We are running Galaxy on an Ubuntu 11.10 computer (5 TB, stripped, etc.). We are assembling a small genome (110 Gb). Our dataset isn't directly uploaded, but is accessed from a directory

Re: [galaxy-dev] Error on local galaxy using SAM-to-BAM tool on a cluster

2011-11-03 Thread Jennifer Jackson
___ 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/ Hello Carlos, If what you want is

Re: [galaxy-dev] Looks like actual user breaks splitting

2011-11-03 Thread Duddy, John
I'm not following you - it's been 6 months since I wrote that code ;-} IT looks to me like a DatasetPath() object is always placed in that array, and with one exception near then, it looks like the change I made generates those objects the same way. Do you have a stack trace for the merge

Re: [galaxy-dev] Installing Galaxy on local server

2011-11-03 Thread Jennifer Jackson
Hello Toqa, From your description, this sounds like a local installation for the Galaxy instance itself. Then you can add on a cluster (local or cloud) as needed. Help is under Deploy Galaxy at http://wiki.g2.bx.psu.edu/ Also see the Tool Shed at http://wiki.g2.bx.psu.edu/Tool%20Shed

Re: [galaxy-dev] Looks like actual user breaks splitting

2011-11-03 Thread Nate Coraor (n...@bx.psu.edu)
Duddy, John wrote: I'm not following you - it's been 6 months since I wrote that code ;-} I know the feeling! IT looks to me like a DatasetPath() object is always placed in that array, and with one exception near then, it looks like the change I made generates those objects the same way.

Re: [galaxy-dev] Looks like actual user breaks splitting

2011-11-03 Thread Nate Coraor (n...@bx.psu.edu)
Nate Coraor (n...@bx.psu.edu) wrote: Duddy, John wrote: I'm not following you - it's been 6 months since I wrote that code ;-} I know the feeling! IT looks to me like a DatasetPath() object is always placed in that array, and with one exception near then, it looks like the change I

Re: [galaxy-dev] Clusters, Runners, and user credentials

2011-11-03 Thread Fields, Christopher J
On Nov 3, 2011, at 9:50 AM, Nate Coraor wrote: Hi Chris, Ilya's solution uses sudo to submit the job via drmaa after switching to the actual user's uid and gid. This means giving your Galaxy user sudo rights to run 3 scripts as root: * A script to submit jobs * A script to kill