- galaxy-dev - lists.galaxyproject.org

June 3, 2013 Galaxy Distribution
by Jennifer Jackson 04 Jun '13

04 Jun '13

June 3, 2013 Galaxy Distribution <http://wiki.galaxyproject.org/News/2013_06_03_Galaxy_Distribution> *Complete News Brief <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_03>* *Highlights:* * Visualization tool updates to Scatterplot <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#Scatterplot> and Trackster <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#Trackster>. * Job distribution, error tracking/management, and reporting function improvements to Admin <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#Admin> & Core <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#Core>. * Multiple Tool <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#Tools> updates, History and Dataset <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#Histories> upgrades, and other related UI <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#UI> enhancements. * New features and fixes added to the Tool Shed <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#Tool_Shed> and related components. * Python 2.5 Support /officially ended/ <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#Python_2.5_Support_H…>. * Plus newly merged Pull Requests <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#Pull_Requests_Merged> and links to tickets covering key Bug Fixes <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#Bug_Fixes>. / http://getgalaxy.org/ /http://bitbucket.org/galaxy/galaxy-dist/ /http://galaxy-dist.readthedocs.org/ // new: $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable upgrade: $ hg pull $ hg updaterelease_2013.06.03 /Thanks for using Galaxy,/ The Galaxy Team <http://wiki.galaxyproject.org/Galaxy%20Team>

1 0

Problem with tool in R
by Ramon Tiburski 03 Jun '13

03 Jun '13

I have a problem with a tool in R. I can't load the RPostgreSQL library that I get the following error: ERROR: carregando pacotes exigidos: dbi My xml is this: <command interpreter="bash">r_wrapper.sh $script_file</command> <configfiles> <configfile name="script_file"> library(RPostgreSQL) ... </configfile> </configfiles> I have this library installed at my system, what can I do?

2 1

Information for Galaxy Event Horizon
by Sarah Maman 03 Jun '13

03 Jun '13

Dear all, Four days of training in genomics are occurring on our local instance of Galaxy (27-30 May). This training session takes place at INRA, Toulouse Auzeville, France, as part of a collaboration between Sigenae (http://www.sigenae.org/) and GenoToul bioinformatics platform (http://bioinfo.genotoul.fr/) This session is composed of four training days: * Galaxy first step * Reads alignment and SNP calling * RNAseq alignment and transcripts assemblies * sRNAseq Do you think it is possible to list our training session in your "Galaxy Event Horizon"? Sincerely, Sarah Maman -- --*-- Sarah Maman INRA - LGC - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 --*--

2 1

storage utilisation on the main galaxy instance
by Nikolay N. 03 Jun '13

03 Jun '13

Hi, I had storage utilisation of +60% and two days ago I decided to remove a large chunk of my data. I did this by clicking on the "delete" links for each of these datasets. Today I've logged in and see that my storage utilisation hasn't changed. Is there anything else that I need to do to free up the storage? many thanks, Nick

1 0

Stable usegalaxy.org links for main Tool Shed repositories?
by Peter Cock 03 Jun '13

03 Jun '13

Hello all, Having asked this before, I knew the friendly and memorable alias http://usegalaxy.org/toolshed/ existed for the main Galaxy Tool Shed, http://toolshed.g2.bx.psu.edu Currently tools there have a unique stable shareable URL like this: http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus (Due to the current frame based design, that redirects to a less pleasant URL) >From a little experimentation, the following style aliases also work: http://usegalaxy.org/toolshed/view/devteam/ncbi_blast_plus Is that deliberate? Can it be relied on, and are these style URLs actually preference? If so, could the Tool Shed be enhanced to allow a default stem for the URL (rather than the current host name) to show these URLs instead? (Personally I find the usegalaxy.org based URLs more presentable compared to toolshed.g2.bx.psu.edu which feels less permanent.) Thanks, Peter

1 0

Run galaxy on a specific SGE queue
by Sarah Maman 03 Jun '13

03 Jun '13

Hi everyone, Galaxy is set up on our cluster, and so far everything is working just fine. However, we'd like to change the submission queue from the default to a specific one. To do so, we tryed to set on the universe_wsgi.ini file the default_cluster_job_runner parameter as following: default_cluster_job_runner = drmaa://-q test.q -l mem=8G -l h_vmem=10G/ When doing so, an error occured telling us the job has been rejected because 2 queues were specified: the workq (default one) and the test.q. Should be the queue setting this way ? What are we doing wrong ? thanks for your help, Sarah -- Sarah Maman INRA - LGC - SIGENAE Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53

3 2

FW: order of menu items
by Stephanie LE GRAS 03 Jun '13

03 Jun '13

Dear all, We have 2 different instances of Galaxy within our institute (a test and a production instance). The thing is that the two tool menus are not in the same order and we don't understand why because we've got the same configuration files on both instance. Test instance [cid:1A999B49-4E2D-4B03-A0C8-0F3E7459F730] Production instance: [cid:31D3C34C-1FF2-4ED9-8A0D-DF73DEE548A7] What could explain a difference in the order of the menu items? The thing is that I would like to get the NGS tools all together. Thank you in advance. Stephanie -- Stephanie Le Gras Bioinformatics engineer High throughput sequencing platform IGBMC 1, rue Laurent Fries 67404 ILLKIRCH Cedex France Tel. : +33 (0)3 88 65 32 73 Tel. Solexa : +33 (0)3 88 65 32 97

2 2

BWA installation
by מירב . 03 Jun '13

03 Jun '13

Hello all, I am trying to install BWA , I used the command: " bwa index -a bwtsw /global_data/hg18full.fa " and I got only 5 files insted of 8 The missing files are - rbwt - rpac - .rsa I didn't recieve any error message while running. thanks for your help merav

3 3

problem with current galaxy to submit job to drmaa/sge
by tin h 01 Jun '13

01 Jun '13

Hello galaxy-dev gurus, I was trying to upgrade my galaxy server... I removed the old galaxy-dist and ran hg clone https://bitbucket.org/galaxy/galaxy-dist/ restored universe_wsgi.ini file and various tool-data config, and tried to restart galaxy. After some twiddling, I see the error message at the end of this email. The strangest thing I see is this /usr/prog/galaxy/galaxy-dist/eggs/drmaa-0.4b3-py2.6.egg/drmaa/wrappers.py on my current system, drmaa-0.4b3-py2.6.egg is a file and not a directory... is the latest code that I just downloaded corrupted or something? Much thanks in advance for your help in this matter. -Tin PS. Relevant entry in universe_wsgi.ini on cluster config: start_job_runners = drmaa default_cluster_job_runner = drmaa:/// galaxy.tools.genome_index DEBUG 2013-05-24 08:42:49,150 Loaded genome index tool: __GENOME_INDEX__ galaxy.jobs.manager DEBUG 2013-05-24 08:42:49,153 Starting job handler galaxy.jobs.runners DEBUG 2013-05-24 08:42:49,155 Starting 4 LocalRunner workers galaxy.jobs DEBUG 2013-05-24 08:42:49,156 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' Traceback (most recent call last): File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 35, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/app.py", line 159, in __init__ self.job_manager = manager.JobManager( self ) File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/manager.py", line 31, in __init__ self.job_handler = handler.JobHandler( app ) File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 29, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 543, in __init__ self.job_runners = self.app.job_config.get_job_runner_plugins() File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 486, in get_job_runner_plugins rval[id] = runner_class( self.app, runner[ 'workers' ], **runner.get( 'kwds', {} ) ) File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 75, in __init__ self.ds.initialize() File "/usr/prog/galaxy/galaxy-dist/eggs/drmaa-0.4b3-py2.6.egg/drmaa/__init__.py", line 274, in initialize _w.init(contactString) File " /usr/prog/galaxy/galaxy-dist/eggs/drmaa-0.4b3-py2.6.egg/drmaa/wrappers.py", line 59, in init return _lib.drmaa_init(contact, error_buffer, sizeof(error_buffer)) File "/usr/prog/galaxy/galaxy-dist/eggs/drmaa-0.4b3-py2.6.egg/drmaa/errors.py", line 90, in error_check raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value)) DrmCommunicationException: code 2: range_list containes no elements

2 2

Re: [galaxy-dev] [galaxy-user] List of genomes
by Jennifer Jackson 01 Jun '13

01 Jun '13

Hello Yongde, The list of genomes is gathered from many sources and is comprehensive to facilitate external display functionality (at UCSC - main and microbial-, Ensembl, Wormbase, etc.). When assigning a dataset in a standard format to one of these sources, those available will appear as links within the dataset's box. Trackster (Galaxy's native visualization tool) is available to most common data formats, even in the absence of an assigned database, through the use of the Custom Reference Genome function (aka "Custom Build"). We think this is a great advantage, in particular for cases such as yours - since you don't have restrict yourself to external applications that happen to host your genome. Click on the link here and select "Trackster" to give it a test run: The Custom Reference Genome function is also intended to be used for smaller genomes such as this one when performing alignments and most other jobs - no pre-indexing of the genome is necessary. Simply load the genome in fasta format as a dataset and use it with tools, using a "reference genome from the history". The rational is that these are many, small, easily indexed during the course of job processing, and provides immediate access to genomes that are either newly published, or not widely used, or simply too numerous as a whole class for us to practically process in full and keep current. We have detailed help about how to use the Custom Reference Genome method, including troubleshooting help should you need it, although in practice you will likely find this to be fairly simple with 2-3 preparatory steps, depending on the source. Most if not all of these can be done within Galaxy. http://wiki.galaxyproject.org/Support#Custom_reference_genome Hopefully this helps. If you do need more guidance, please let us know, Best, Jen Galaxy team On 4/29/13 9:01 AM, YBao wrote: > Hi All, > > I was trying to map a set of data to a genome, Klebsiella pneumoniae > subsp. Pneumoniae MGH 78578(31). While uploading the reads, I was able > to find the reference genome as listed above. However, when I tried to > map the data using wither bowtie or BWA, the pull down list did not > include this genome. Can someone help or enlighten me as why it did > not make into the list? > > Thanks > > Yongde > > -- > Yongde Bao > DNA Sciences Core > Dept. of Microbiology, Immunology, > and Cancer Biology > UVA > > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

2 1