June 2013 - galaxy-dev - lists.galaxyproject.org

Creating workflow which includes Multifile upload
by Alex.Khassapov＠csiro.au 05 Jun '13

05 Jun '13

Hi John, One more problem with multifile upload - when I display a workflow which includes multi upload tool, I get: Module workflow_run_mako:476 in render_row_for_param >> <http://140.79.7.98/workflow/run?id=f597429621d6eb2b> __M_writer(unicode(param.get_label())) AttributeError: 'UploadDataset' object has no attribute 'get_label' Ok, I see that UploadDataset class is derived from Group, not ToolParameter. So I tried to add get_label() to the Group class, which returns some string. But then I get: Module workflow_run_mako:476 in render_row_for_param >> <http://140.79.7.98/workflow/run?id=f597429621d6eb2b> __M_writer(unicode(param.get_label())) TypeError: 'str' object is not callable Here my knowledge of Galaxy ends and I need some help please. -Alex

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Local instance - Problem when log in/out
by Stephanie LE GRAS 05 Jun '13

05 Jun '13

Hi everyone, We have set up a local instance of Galaxy within our research institute and we are encountering an error when logging in/out. I've attached a screenshot of what's displayed on the screen when I log out. It is kind of a double galaxy menu and we don't understand why it is like this. [cid:7DC11615-6B60-474B-BD6E-6C118D96826D] After logging out: If you click on the link "go to home page", then you're re-directed to the login page. When logging in, it's working and no more trouble. But if you click on the link "Go back to the page you were visiting", you are re-directed to the login page. And when you log in over, you arrive one more time on a page with a double menu, an error pop up comes out (see attached Error.png) and finally, you're redirected to the login page again. Once you log in again, you can finally start working using Galaxy. Error: [cid:17FFC87F-7D93-43A8-AF3A-35E69332C685] Has someone already encountered such an error? Do you know how we could solve it? We would like to get the same behavior as it is on the Galaxy main instance knowing that only registered user can use our Galaxy local instance. Thank you in advance for your help. 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

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Internal Server Error during installation of ncbi_blast_plus
by Keilwagen, Jens 05 Jun '13

05 Jun '13

Hi guys, we are currently estalishing our own local Galaxy instance. However, when we try to install "Repository 'ncbi_blast_plus'" from the Galaxy main tool shed via the admin pages, we obtain the following error "Internal Server Error Galaxy was unable to sucessfully complete your request An error occurred. This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. The error has been logged to our team." We tried to install on three different days. Hence, we believe there might be another problem. Thanks for any help. Best regards, Jens

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Adding a Tool for PANAMA
by Saket Choudhary 05 Jun '13

05 Jun '13

As part of a warmup, I added a tool for perming eQTL analysis using PANAMA( http://ml.sheffield.ac.uk/qtl/panama/) By default PANAMA writes to stderr and creates a PANAM_results.csv file in the same directory as the input files. I wrote a python wrapper https://bitbucket.org/saketkc/galaxy-central/src/3eb26205af5a0b77fa6177d5ec… for this. I however also came across how stderr text can be handled in Galaxy : http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cstdio.3E.2C_… and thus wrote a new XML : https://gist.github.com/saketkc/5697388 Apparently the above XML runs too, but I dont get back a CSV. Essentially I need to move the PANAMA_results.csv file to output1. Can this be done without using a wrapper at all , just using the XML files ? Is there a way to nest the commands in the XML so that I could do a <move command> after <panama command> , but how would the paths be specified ? Saket

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mapping Summary from Bowtie
by sridhar srinivasan 05 Jun '13

05 Jun '13

Dear Developers, I am running Bowtie2 through galaxy interface, previously it gives the the mapping summary and convert the format to sam.. but now it directly convert the fastq file to bam and doesnt give the mapping summary. how to get the mapping summary from bowtie2 using galaxy interface.. Thanks Sridhar

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GCC2013 Regular Registration closes June 14
by Dave Clements 04 Jun '13

04 Jun '13

Hello all, This is a reminder that registration<http://wiki.galaxyproject.org/Events/GCC2013/Register>for the 2013 Galaxy Community Conference (GCC2013<http://wiki.galaxyproject.org/Events/GCC2013>) closes June 14*, just ten days from today. *Registering now<http://wiki.galaxyproject.org/Events/GCC2013/Register>avoids the 100% late registration surcharges, and guarantees you a spot in the Training Day sessions<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay>you want to take. *Registration is still a bargain with the full 3-day registration starting at ~ €165 for post-docs and students (that is just €55 per day). The program <http://wiki.galaxyproject.org/Events/GCC2013/Program> features 15 Training Day sessions<http://wiki.galaxyproject.org/Events/GCC2013/Program#Day_0:_Training_Day.2C…> in 5 tracks on 12 different topics, 25 Talks<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts#Talk_Abstracts> on topics ranging from Reproducibility<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts#Events.2FGCC2013.2FA…> to Exploiting Galaxy<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts#Events.2FGCC2013.2FA…> , 23 Posters<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts#Poster_Abstracts> (and counting), 2 Lightning Talk sessions, and a end-of-conference event at an historic venue high above Oslo. GCC2013 is a great opportunity to share best practices from and network with other researchers also facing the challenges of data-intensive biology. Ser frem til å se deg i Oslo! GCC2013 Organizing Committee PS: and please help get the word out<http://wiki.galaxyproject.org/Events/GCC2013/Promotion> . * Not June 7, as had been stated earlier in several places. -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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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>

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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?

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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 --*--

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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

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