October 2011 - galaxy-dev - lists.galaxyproject.org

galaxy citation_url setting
by Shantanu Pavgi 03 Nov '11

03 Nov '11

Hi, It seems like modification of 'citation_url' in the universe_wsgi.ini config file has no effect in the UI (Help --> How to Cite Galaxy). Is it something hard-coded in the source? -- Thanks, Shantanu.

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GeneTrack-Installation - Version?
by Stefanie Ververs 03 Nov '11

03 Nov '11

Hi everybody, we're hosting our own galaxy instance and the next step should bei the integration of GeneTrack. (Not the tool, that is already included, but the browser, which has to be set up on our own, as i could read on the mailing list.) I've been reading all information on http://genetrack.bx.psu.edu and http://atlas.bx.psu.edu/genetrack/docs/genetrack.html - but I do not really get, which is the current, newest version? The only one to download is available at googlecode (1.0.3) and - according to the information on http://genetrack.bx.psu.edu - there is a newer one (2.0) I tried to run the tests for 1.0.3 but some fail - the logs aren't quite clear about the problem, even on Debug-mode. Could you tell me what version to use and which instructions? Are there limits or other dependencies according to the used python-packages? Hoping for help & thanks in advance, Steffi

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Local Galaxy Instance MarkupSafe error
by Mickael ESCUDERO 03 Nov '11

03 Nov '11

Hi there, I'm getting exactly the same problem with any job running on a TORQUE/PBS cluster. The jobs actually run fine as I can see the output and download it, but it's marked as failed in the galaxy history, with the following message: WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched The command `python -ES ./scripts/fetch_eggs.py` gives nothing as output. If I run the same tools locally there is no problem. Cheers Micka > Message: 5 > Date: Thu, 27 Oct 2011 15:08:17 +1100 > From: Jerico Nico De Leon Revote <jerico.revote(a)monash.edu> > To: galaxy-dev(a)lists.bx.psu.edu > Subject: [galaxy-dev] Local Galaxy Instance MarkupSafe error > Message-ID: > <CAP9ULhYiPxYB2CWtqOSM3MquUu55ARxY5poR1dBaHEj1UcO8UQ(a)mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > I'm just doing a simple get->data from UCSC on our local Galaxy > instance and got the following error: > > WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) > cannot be fetched > > The job box then is displayed as red on the history panel. > The job runner states that the job finished normally on the cluster. > Galaxy is checkout from galaxy-central (changeset: 6176:34fffbf01183). > > Thanks, > > Jerico >

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Re Acutal user code
by Chorny, Ilya 03 Nov '11

03 Nov '11

Nate, I have been trying to figure out how to make the changes you suggested (i.e. write output files to the job_working_directory) and then move them over to files but I am having a difficult time navigating the code. If you could point me in the right direction, that would be helpful. I know the lib/galaxy/models/__init__.py initializes the output files but I don't think that is the right place to make the change. This change probably needs to be done in the Job_Wrapper but most of the code is very cryptic to me. Any guidance would be greatly appreciated. These changes should not take very long to implement once I get a handle on the code. Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny(a)illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>

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getting job's index position in the history from database
by Shantanu Pavgi 02 Nov '11

02 Nov '11

I am trying to get job's index in the history panel using SQL query (index number shown in the history when a job is submitted). I am unable to locate the necessary table-column for it. Any pointers in which table-column it is located will be really helpful. -- Thanks, Shantanu.

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Providing Data to Galaxy Users
by Ostell, Jim (NIH/NLM/NCBI) [E] 02 Nov '11

02 Nov '11

Hello Galaxy Folks, NCBI has received a few requests to provide a mechanism for people browsing the NCBI databases to download the data they have selected into Galaxy, so we are looking into it. I know some other sites have done this, it looks like through a URL based callback mechanism. However, I know things can change over time, and I'd like to be sure that we are assessing an approach that reflects your current best thinking, whether it turns out to be something well established you are happy with, or if you might be considering moving toward something new, we'd like you to tell us what you think would work best for your users in your environment. If you can just point me at a URL with the appropriate documentation, that's great. If you'd prefer to dialog a little, we're happy to talk. If there is a particular person we should be talking to, let me know. Thanks for your help. Regards, Jim Ostell James M. Ostell, Ph.D. Chief, Information Engineering Branch National Center for Biotechnology Information, NLM, NIH Bldg 45, Rm 5AN.44A 45 Center Drive Bethesda, MD 20892-6510

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data set import into current history
by Oren Livne 02 Nov '11

02 Nov '11

Dear All, Is there an API call for importing data sets into the current history (or a new history)? This feature exists in the web UI. Thanks so much, Oren

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Appropriate method of coalescing tool output (not workflow)
by Jesse Erdmann 01 Nov '11

01 Nov '11

I have an in-house Perl tool that generates a double digit number of outputs that we'd like the user to have access to, but don't necessarily need to be in the history. A complicating factor is that the exact number is determined at run time as user input can add any number of outputs that can't be determined in the scope of the tools' XML processing. Ideally, the end result would be that executing the tool would produce a single output in the history with the other files either being hidden or in the extra_files path. The visible file should be an HTML file that can be used to describe and link to the other outputs as well as providing the option to either unhide or add the hidden outputs to the history for use in subsequent analysis. I've looked at composite datatypes, but as far as I can tell the documentation and examples don't cover how to produce a composite datatype with a variable number of outputs. I briefly tried to use the deprecated <code> tag to iterate over the results with the other outputs added as hidden extra files to the index after execution, but wasn't really excited about using a deprecated feature and couldn't get it working quickly, regardless. Any other suggestions? -- Jesse Erdmann Bioinformatics Analyst Masonic Cancer Center University of Minnesota jerdmann(a)umn.edu 612-626-3123

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Running galaxy on external hard drive
by Alessia D 01 Nov '11

01 Nov '11

Hi, I am very new to Galaxy and so far have only used the online interface. However, I have an old Unix-running computer and I was hoping to run Galaxy as a local instance. However, the computer has a very small hard drive, that is already half full, so I was wondering if there is any way I can run Galaxy by installing it on an external hard drive. I tried already, and was able to install it properly and connect, but I get errors when I try to upload data. Any help would be greatly appreciated. I don't have a lot of experience with Unix systems, so it might be something easy to solve or impossible to do, I have no idea. Thanks! Alessia

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Upcoming Galaxy Events
by Dave Clements 31 Oct '11

31 Oct '11

Hello all There are several Galaxy related events going on at Cold Spring Harbor Laboratory in November, but if you aren't already registered for those it is now too late to get in. However, there are several deadlines in November and events in the coming months. See the Events<http://wiki.g2.bx.psu.edu/Events>page ( http://wiki.g2.bx.psu.edu/Events) for a full listing of upcoming events. If you have a Galaxy related event please send it to outreach(a)galaxyproject.organd we will help you get the word out. Date Topic/Event Venue/Location Contact November 2-5 Best practices for variant discovery through Galaxy: Oscillating evolution within dual coding genes <http://meetings.cshl.edu/meetings/info11.shtml> Genome Informatics 2011 <http://meetings.cshl.edu/meetings/info11.shtml>, Cold Spring Harbor, New York, United States Dan Blankenberg <http://wiki.g2.bx.psu.edu/dan> November 8-21 Advanced Sequencing Technologies & Applications Course<http://meetings.cshl.edu/courses/c-seqtech11.shtml> Features Galaxy and much more. Cold Spring Harbor Laboratory, New York, United States James Taylor <http://wiki.g2.bx.psu.edu/JamesTaylor> November 9-15 Compuational & Comparative Genomics Course<http://meetings.cshl.edu/courses/c-ecg11.shtml> Features Galaxy and much more. Cold Spring Harbor Laboratory, New York, United States James Taylor <http://wiki.g2.bx.psu.edu/JamesTaylor> January 8-21 2012 2012 Workshop on Genomics<http://evomics.org/workshops/workshop-on-genomics/2012-genomics-cesky-kruml…> Features Galaxy and much more. *Application deadline is November 1.* Český Krumlov, Czech Republic James Taylor <http://wiki.g2.bx.psu.edu/JamesTaylor> January 14-18 2012 Galaxy Session @ GMOD Workshop PAG 2012 <http://www.intlpag.org/>, San Diego, California, United States Dave Clements <http://wiki.g2.bx.psu.edu/DaveClements> January 17 2012 Reproducible workflows for next generation sequencing analysis<http://www.nowgen.org.uk/facilities/events/event.php?id=30> Nowgen <http://www.nowgen.org.uk/>, University of Manchester<http://www.manchester.ac.uk/>, United Kingdom Tom Hancocks <training(a)nowgen.org.uk> Thanks, Dave Clements <http://wiki.g2.bx.psu.edu/DaveClements> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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