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

Wrapping web-tools
by Franco Caramia 07 Nov '12

07 Nov '12

Hi list, I¹m trying to find documentation or examples on how to wrap web-tools (like primer3, optimus primer) in Galaxy. Any useful links or examples would be of great help. Thanks, Franco This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.

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MrBayes wrapper - set parameters through Galaxy?
by Gomez, Ann 06 Nov '12

06 Nov '12

Hello all, I've written a MrBayes wrapper that accepts a Nexus file (presumably containing a data block and a command block). In order to make it a bit easier for new users, I was hoping to be able to let users specify some parameters, such as their model, in Galaxy, as opposed to including it in the command block of the Nexus file. Am I correct in thinking this is not possible since MrBayes does not have a way to invoke commands in-line? To clarify for non-MrBayes people, my limited understanding is that you either invoke the interpreter with "$ mb" and then enter your commands, or directly execute a Nexus file (containing the data and commands) with " $ mb <nexusfilename>". Please correct me if I'm missing something or thinking about this completely wrong. I'd appreciate any input about MrBayes or a similar kind of tool. Cheers, Ann Ann Gomez Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada KW Neatby Bldg | éd. KW Neatby 960 Carling Ave| 960, avenue Carling Ottawa, ON | Ottawa (ON) K1A 0C6 E-mail Address / Adresse courriel: ann.gomez(a)agr.gc.ca <mailto:ann.gomez@agr.gc.ca> Telephone | Téléphone 613-759-6805 Facsimile | Télécopieur 613-759-1701 Government of Canada | Gouvernement du Canada

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Sequences are not currently available for the specified build
by Scooter Willis 06 Nov '12

06 Nov '12

Trying to use aaChanges with 1. Running Galaxy at revision: 8150:b996950ffcf2<http://bitbucket.org/galaxy/galaxy-central/changesets/b996950ffcf2> Both input files have hg19 for the Database/Build. Should this work as configured or do I need to upload the HG19 Fasta data and do something in particular? I found this question asked multiple times in the discussion forums related to custom genomes and a mention here from June 2012 that Hg19 is short-listed which sounds like as of June it isn't setup. Hi Rich, Additional genomes will be specially sorted, indexed, and added to the GATK tool suite as it moves out of beta status. Hg19 is short-listed for addition near term. We do take requests to have genome added to tools and consider these when ranking our prioritization lists. Which genome did you want to use? One small warning when using a custom reference genome with this particular tool set - be sure to visit the GATK web site links directly to understand the sorting criteria for genomes. It can be different than how Galaxy, UCSC, and many of the existing tools already sort or instruct users to sort genomes or data. In short, the genome must be sorted in the exact order that it was originally released, but even this can be slightly confusing, especially if working with a non-human genome as there are few examples. Still, the documentation can help and tools are easily tested (if the sorting is wrong, the tool will fail and let you know). If others have requests for GATK native genomes, they are also welcome to reply. In general, key model organisms would be ranked highest in priority. We also try to get the largest genomes loaded natively first (for purely practical reasons). Good question, thanks! Jen Galaxy team [cid:039EC436-2F38-40C6-A4FD-972B34755E16]

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Regarding Job Running Isuue
by BONNY PATEL 06 Nov '12

06 Nov '12

Hi I am trying to map my Chip-Seq data using Bowtie for Illumina. It's been two days my job status is "Job is waiting to run". Can please tell me why its taking so much time ?? regards, -----BONNY

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Regarding Data not geting analyze
by BONNY PATEL 06 Nov '12

06 Nov '12

Hi , I am trying map my Chip-Seq data with Bowtie for Illumina. It's been two day and my job status is "Job still waiting to run" Please help me why my job is taking too much time to run ???? ------BONNY PATEL

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language inside <command> tag set
by Kevin Y 06 Nov '12

06 Nov '12

Hi, I'm looking for documentation on what I can do inside the <command> tag for tools. I know of things like #if str( $input ) == 'yes': Do stuff #end if can I do for loops? What should I google? I can't find anything on the wiki. Thanks, Kevin.

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Unnamed histories proliferating, can't get to my data
by Karger, Amir 05 Nov '12

05 Nov '12

I'm using Galaxy from June, 2012. (Sorry if there's already a fix.) We've got it "working" in production. We've gotten whole pipelines to run. However, we occasionally get situations where we upload file (using the FTP mechanism), which seems to be fine, but then I can't get to the data. I went to Saved Histories, and selected Switch, and it outlined the line in blue and wrote "current history" next to it. But the right pane still shows "Unnamed history" with no data in it. Then if I go back to Saved Histories, I get one or two new Unnamed histories, created within the last few minutes. I just tried to "View" the history, which worked (in the middle pane) and clicked "import and start using history". This seemed to work, but I got three panes inside the middle pane! When I go back (again) to saved histories, there are 3 histories - one the imported one with 2 steps, two unnamed histories, all created < 1 minute ago. We just asked a beta tester to play with things, and he uploaded two fastqs, but had what sounds like a similar problem. Any thoughts on what's happening? Thanks, -Amir Karger Research Computing Harvard Medical School

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xgrid cluster computing
by Edward Hills 05 Nov '12

05 Nov '12

Hi Galaxy team, So our university has decided to switch our xgrid clusters back on and we are looking to set Galaxy up on these. Has anyone got (or tried) to set up Galaxy on xgrid before? xgrid supposedly conforms to DRMAA so technically Galaxy should work, correct? Cheers, Ed

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Think I found a bug
by Juan González-Vallinas 05 Nov '12

05 Nov '12

Hi galaxy devs, We are in the final stages of deploying a new Galaxy instance. We downloaded the galaxy-dist version a month ago aprox. We realized that, when launching a job and deleting it in the middle of the execution (hitting the Delete button in the history bar) will output the following error in the logger: galaxy.jobs.handler DEBUG 2012-11-05 15:56:33,537 Stopping job 45: galaxy.jobs.handler DEBUG 2012-11-05 15:56:33,537 stopping job 45 in local runner galaxy.jobs.handler ERROR 2012-11-05 15:56:33,538 Exception in monitor_step Traceback (most recent call last): File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py", line 298, in monitor self.monitor_step() File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py", line 341, in monitor_step self.dispatcher.stop( job ) File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py", line 438, in stop self.job_runners[runner_name].stop_job( job ) File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 180, in stop_job if job.get_external_output_metadata(): AttributeError: 'Job' object has no attribute 'get_external_output_metadata' By copying the definition of get_external_output_data from the Task class into the Job class, we fixed the problem and now the jobs are terminated successfully. This is the code I added: class Job( object ): ... def get_external_output_metadata( self ): return None ... In this file: https://bitbucket.org/galaxy/galaxy-central/src/9d6a61f060d359a0289b3163990… Do you think this fix is correct, or is it a potential problem? Also, sorry I sent you through this channel, I couldn't find the way of reporting this on BitBucket. Regards, -- Juan González-Vallinas PhD Student Regulatory Genomics Group Research Unit in Biomedical Informatics (GRIB) Universitat Pompeu Fabra (UPF) Barcelona Spain (Currently visitor at UPenn)

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How to add the option "-c enabled" to the qsub command?
by Luobin Yang 05 Nov '12

05 Nov '12

Hi, guys, I would like to enable checkpoint and restart for some galaxy jobs. In order to do that, I need to add "-c enabled" option when using "qsub" to submit a job. What files should I change to add this option? I am using Torque PBS job runner. Thanks, Luobin

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