May 2012 - galaxy-dev - lists.galaxyproject.org

HMMER wrappers
by Peter Cock 26 Jul '12

26 Jul '12

Hello all, Has anyone done a wrapper for HMMER2 or HMMER3? http://hmmer.janelia.org/software I can't find anything in the Tool Shed http://toolshed.g2.bx.psu.edu/ so we are likely to look into doing this ourselves - starting with hmmerscan. Thanks, Peter

4 16

output file
by 張詩婷 19 Jul '12

19 Jul '12

Hi, After execution, my tool created many files in a directory , how can I to find this directory? command: bash mytool.sh $input

2 1

Galaxy not killing split cluster jobs
by Peter Cock 10 Jul '12

10 Jul '12

Hi all, We're running our Galaxy with an SGE cluster, using the DRMAA support in Galaxy, and job splitting. I've noticed if the user cancels a job (that was running or queued on the cluster) while the job is shows as deleted in Galaxy, looking at the queue on the cluster with qstat shows it persists. I've not seen anything similar reported except for this PBS issue: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-October/003633.html When I don't use job splitting, cancelling jobs seems to work: galaxy.jobs.handler DEBUG 2012-05-01 14:46:47,755 stopping job 57 in drmaa runner galaxy.jobs.runners.drmaa DEBUG 2012-05-01 14:46:47,756 (57/26504) Being killed... galaxy.jobs.runners.drmaa DEBUG 2012-05-01 14:46:47,757 (57/26504) Removed from DRM queue at user's request galaxy.jobs.runners.drmaa DEBUG 2012-05-01 14:46:48,441 (57/26504) state change: job finished, but failed galaxy.jobs.runners.drmaa DEBUG 2012-05-01 14:46:48,441 Job output not returned from cluster When I am using job splitting, cancelling jobs fails: galaxy.jobs.handler DEBUG 2012-05-01 14:28:30,364 stopping job 56 in tasks runner galaxy.jobs.runners.tasks WARNING 2012-05-01 14:28:30,386 stop_job(): 56: no PID in database for job, unable to stop That warning comes from lib/galaxy/jobs/runners/tasks.py which starts: def stop_job( self, job ): # DBTODO Call stop on all of the tasks. #if our local job has JobExternalOutputMetadata associated, then our primary job has to have already finished if job.external_output_metadata: pid = job.external_output_metadata[0].job_runner_external_pid #every JobExternalOutputMetadata has a pid set, we just need to take from one of them else: pid = job.job_runner_external_id if pid in [ None, '' ]: log.warning( "stop_job(): %s: no PID in database for job, unable to stop" % job.id ) return pid = int( pid ) ... I'm a little confused about tasks.py vs drmaa.py but that TODO comment looks pertinent. Is that the problem here? Regards, Peter

3 9

Interested in speaking with other institutions deploying Galaxy locally?
by Ann Black-Ziegelbein 05 Jul '12

05 Jul '12

Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein

22 32

Looking for recommendations: How to run galaxy workflows in batch
by Dave Lin 05 Jul '12

05 Jul '12

Hi All, I'm looking to batch process 40 large data sets with the same galaxy workflow. This obviously can be done in a brute-force manual manner. However, is there a better way to schedule/invoke these jobs in batch 1) from the UI with a plugin 2) command-line 3) web-service Thanks in advance for any pointers. Dave

5 8

Exporting histories through API
by Martin Dahlö 25 Jun '12

25 Jun '12

Hello there As the subject hints, I am trying to export histories through the API. Doing it through the web interface is a breeze, but has it been implemented in the API yet? I could not find anything about it in the examples or by searching the web/this list. I am planning to only use Galaxy through the API to import my data and run some workflows on it, and then export the results. Preferably specific files from the history, but a bundled history like the one you get from the web interface 'Export history' would be ok as well. Has anyone done something like this, and can point me in the right direction? :) Mvh Martin Dahlö --- Bioinformatic support martin.dahlo(a)scilifelab.uu.se +46 18 611 59 59 +46 706 70 79 55 http://www.scilifelab.uu.se/ http://www.uppnex.uu.se ---

3 3

Workflow API (runtime modification of tool parameters)
by Richard Park 21 Jun '12

21 Jun '12

Hello, I was wondering what would be the best way to extend Galaxy's API functionality to allow for runtime modification of tool parameters? I have successfully been able to run workflows programmatically using the API, following the basic steps in: scripts/api/execute_workflow.py. scripts/api/example_watch_folder.py However, it is unclear to me, what would be the best way to run workflows through API with specific parameters at various steps. Should I generate new workflows for every workflow that requires different parameters and upload this to galaxy? Or would it be better to extend the API to allow for runtime parameter configuration? If this is the case, any pointers on how to extend this would be greatly appreciated. Thank you, Richard Park

2 7

Configuring Galaxy for FTP upload
by Ciara Ledero 12 Jun '12

12 Jun '12

Hi all, According to Galaxy, uploading files larger than 2GB will surely fail. For this reason, uploading via FTP is recommended. Unfortunately, I cannot download/install an FTP server for Galaxy since I am working on a remote server. I only have access to it via Xming. Is there anyway to allow FTP upload, without using ProFTPd? Can I use Mozilla's fireFTP or Linux's own FTP? (Actually, I tried to connect to Galaxy, but I was denied access.). Thank you in advance for any help. CL

3 7

Task Manager: This Galaxy instance is not the job manager.
by Dave Lin 11 Jun '12

11 Jun '12

Dear Galaxy Team, I've been getting the following error for some time when I try to access the Manage Jobs Task. "This Galaxy instance is not the job manager. If using multiple servers, please directly access the job manager instance to manage jobs." For debugging purposes, I'm only running the single master instance. I'm using CloudMan/Amazon EC2. I traced the code and suspect it might have something to do with an Amazon IP Address/hostname discrepancy, but am not sure how to go about fixing this. On a related note, if I can't access this page, what is the best way to clear/cancel jobs via the command line? Thanks in advance, Dave Thanks, Dave

5 5

Proftpd Problem
by CHEBBI Mohamed Amine 08 Jun '12

08 Jun '12

Hi, I'am trying to set up ProFTP on Debain to enable FTP upload on Galaxy installed locally? I followed the instructions on this link ( http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP) but it doesn't work. When I restart proftpd i get this message : mod_tls_memcache/0.1: notice: unable to register 'memcache' SSL session cache: Memcache support not enabled Thanks, Amine

2 3