Re: [galaxy-dev] use multiple cores in BWA

2012-11-30 Thread Peter Cock
On Thursday, November 29, 2012, Fenglou Mao wrote: I can use aln -t n to ask BWA to use multiple cores if I run it in command line, in Galaxy, I did not find this option even i tried Full Parameter List, anyone know how to do it? (I installed a local Galaxy server with 64 cores, I want to use

Re: [galaxy-dev] Which version of GATK work with Galaxy?

2012-11-30 Thread Gianmauro Cuccuru
On 11/29/2012 11:09 PM, Fenglou Mao wrote: When I use an old version of GATK, it failed with a report -nt option was not supported, I guess old GATK does not support multi-threading. If I use a new version of GATK, it failed with a report -et NO_ET need a key file to work since new GATK force

Re: [galaxy-dev] Data/history/user export and import

2012-11-30 Thread Bossers, Alex
Jeremy Thanks for the reply and the card :-) Didn't know if it was there or not so that's why the crosspost. I was thinking whether I could establish the same from using the DB access directly!? Or would that be too dangerous? In the past I have tried to transfer the user tables from an old

[galaxy-dev] Workflow loading problem

2012-11-30 Thread Shaun Webb
Hi, I have imported a workflow to my local Galaxy with unrecognised tools. When I try to edit this workflow it will not load. I now realise I have the same problem with some existing workflows where a tool has been removed from Galaxy, I would like to replace these workflow steps without

Re: [galaxy-dev] Changing interface design

2012-11-30 Thread Bossers, Alex
Philippe, As far as I know most of the styling is in galaxydir/static/june_2007_style/blue/base.css or the other stylesheets present in that location. Changes might only be visible when restarting the instance though! Alex Van: galaxy-dev-boun...@lists.bx.psu.edu

Re: [galaxy-dev] Changing interface design

2012-11-30 Thread Philipe Moncuquet
Hi Alex, Thanks a lot for that. I will try next week.. Have a nice weekend. Philippe 2012/11/30 Bossers, Alex alex.boss...@wur.nl Philippe, As far as I know most of the styling is in galaxydir/static/june_2007_style/blue/base.css or the other stylesheets present in that location.

[galaxy-dev] Variable output number in workflows

2012-11-30 Thread Pierre Pericard
Dear all, We've been actively developping xml wrappers for new programs in our instance of Galaxy and we encountered some problems with multiple outputs number while using these tools in a workflow. 1/ In the first case, inputs can be 1 single file or 2 paired files and the program output

Re: [galaxy-dev] Changing interface design

2012-11-30 Thread James Taylor
Also, those files are in fact generated from the .less files in the parent directory. Almost all colors can be customized using an ini file. The best thing to do is to create your own ..._colors.ini file and regenerate the styles into a new directory. You will need nodejs and less to do this. --

[galaxy-dev] December 2012 Galaxy Update

2012-11-30 Thread Dave Clements
Hello all, The December 2012 Galaxy Update is now availablehttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12at http://wiki.galaxyproject.org/GalaxyUpdates/2012_12. *Highlights:* - 37 new papershttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12#New_Papers, including papers on

Re: [galaxy-dev] use multiple cores in BWA

2012-11-30 Thread Fenglou Mao
That will be a pain since so many tools can use multiple cores, and if I edit tool XML file, what will happen is I update Galaxy? Will those edited XML be replaced by the files in Galaxy-dist? Thanks, Frank On Nov 30, 2012, at 3:01 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On

Re: [galaxy-dev] hardware requirement for galaxy

2012-11-30 Thread Dave Clements
Huayan, Take a look at http://wiki.galaxyproject.org/Community/GalaxyAdmins/SurveyResults for an idea of what infrastructure many Galaxy production servers use. That survey was taken this year. I also went to http://galaxyproject.org/search/mailinglists/ and found:

Re: [galaxy-dev] use multiple cores in BWA

2012-11-30 Thread Peter Cock
On Fri, Nov 30, 2012 at 2:54 PM, Fenglou Mao feng...@gmail.com wrote: That will be a pain since so many tools can use multiple cores, and if I edit tool XML file, what will happen is I update Galaxy? Will those edited XML be replaced by the files in Galaxy-dist? If you modify a tool bundled

[galaxy-dev] Issue when enabling use_tasked_jobs with torque and nfs

2012-11-30 Thread Carlos Borroto
Hi, In my environment when I activate 'use_tasked_jobs' I'm getting this message in Info with ncbi_blast wrappers: /local/opt/galaxy/galaxy-dist.8082/database/job_working_directory/000/9/task_0: Job output not returned from cluster Still the dataset with the blast result is green and contains

[galaxy-dev] (no subject)

2012-11-30 Thread Perez, Ricardo
Hi, We are having problems fetching sequences from our mysql database to galaxy. Does anyone know how to do so? Thank you for your help. --Ricardo Perez. ___ Please keep all replies on the list by using reply all in your mail client.

[galaxy-dev] Containing Multiple Datasets in a Single History Item

2012-11-30 Thread Teddy Derego
Today we successfully set up the Barcode Splitter tool to send the outputs directly to the history, but the problem is that in some cases we want to use hundreds of bar codes, which would clutter the history. What I want to do is be able to output a text file containing the names of multiple

Re: [galaxy-dev] hardware requirement for galaxy

2012-11-30 Thread Huayan Gao
Dear Dave, Thanks very much for your reply. It is very useful. Best, Huayan On Fri, Nov 30, 2012 at 11:14 PM, Dave Clements cleme...@galaxyproject.orgwrote: Huayan, Take a look at http://wiki.galaxyproject.org/Community/GalaxyAdmins/SurveyResults for an idea of what infrastructure many