September 2010 - galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] [galaxy-user] Running workflows from the command line
by Erick Antezana 28 Sep '10

28 Sep '10

Hi Nate, Does the API already have workflow support? if so, is there an example somewhere in the Galaxy wiki on how to use the API to run workflows using it? cheers, Erick > Erick Antezana wrote: >> >> Hi, >> >> I was wondering about the status of the implementation that could >> support/enable running wokflows (build using the Galaxy interface) >> from the command line. > > Hi Erick, > > A preliminary version of the API has just been committed to our > development repository last week. However, it does not yet have > workflow support. We hope for this functionality to be added soon. > > --nate > >> >> cheers, >> Erick >> _______________________________________________ >> galaxy-user mailing list >> galaxy-user(a)lists.bx.psu.edu >> http://lists.bx.psu.edu/listinfo/galaxy-user >

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Semi-hidden "advanced" options?
by Peter 28 Sep '10

28 Sep '10

Hi all, Many command line tools have a lot of options - typically there is a short list of main options which will be commonly used, and a larger set of "advanced" options which are rarely used. I'd like to annotate the options in the XML file in this way, so that the "advanced" options are hidden by default. What I have in mind here is something like the NCBI BLAST web interface, where at the bottom of the page there is a little triangle icon next to "Algorithm parameters", clicking on this it expands to show more options. I've been reading the docs and don't see any mention of this kind of thing: http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax Have I missed it, or would this be a feature request? Peter

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Galaxy database user rights
by Peter 27 Sep '10

27 Sep '10

Hello again, [Again, apologies if this is documented somewhere - if it is I haven't found it yet.] I see that for production servers you recommend running Galaxy on PostgreSQL (or maybe MySQL) rather than SQLite: http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer I'm wondering if there is any specific advice about what permissions to give the galaxy database user account beyond this: > Give Galaxy its own database user and database. Galaxy's > schema could conflict with other tables in your database. > Also, restrict Galaxy's database user so it only has access > to its own database. For example, I'd guess that normally (i.e. run.sh) all that Galaxy needs is to insert/delete/modify data in existing tables. On the other hand setup.sh would also need to add/drop/modify tables (particularly for creating the database and also for the database migration system). Does it make sense to have separate PostgreSQL/MySQL accounts for an everyday "galaxy user" (which can't alter the schema, used via run.sh) and a separate "galaxy admin" (used by setup.py)? Or, do you just recommend a single "galaxy" user in PostgreSQL/MySQL which has complete control over the Galaxy database? Simple, but less secure. Thanks, Peter

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File contains inapropriate content
by Andreas Draeger 24 Sep '10

24 Sep '10

Dear Sir or Madam, First of all, I want to thank you for providing the Galaxy framework for runing online programs. It is really cool and works pretty nice. We use galaxy to provide our service SBML2LaTeX, which converts files in the UTF-8-based standard SBML (a specific XML file format) to LaTeX and PDF. However, we are sometimes encountering problems when people try to upload their SBML files on our webservice environment. Often people receive the error message "file contains an inappropriate content". Maybe the reason is that SBML may contain special characters, which are not part of the 1970's ASCII definition. But I don't really know what the problem is. We receive mails from our users quite often and cannot do much because it seems to be a problem of Galaxy. I would therefore like to know if you have a workarround that we can use. To have an example for a file that doesn't work, please consider the following: http://www.comp-sys-bio.org/yeastnet/v4/yeast_4.02.xml. It would be nice to provide me with some helpful information. Cheers Andreas Dräger -- Dipl.-Bioinform. Andreas Dräger Eberhard Karls University Tübingen Center for Bioinformatics (ZBIT) Sand 1 72076 Tübingen Germany Phone: +49-7071-29-70436 Fax: +49-7071-29-5091

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Re: [galaxy-dev] Add a new data type
by Kaiyu Shen 24 Sep '10

24 Sep '10

Hi,Folks: Could someone give me some clues on how to solve this problem: adding a new data type of tar (for uncompressing in the following process)? Thanks

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format of csv for creating forms in Galaxy LIMS
by nsfox＠uwaterloo.ca 23 Sep '10

23 Sep '10

Hi, When making a csv file to create a form from in Galaxy LIMS, you list (from left to right separated by comma): 1.Field Name 2.Field Description 3. ?? 4.Whether the field is required (optional/required) 5.Field Type (TextField, SelectField, etc) 6.Values for SelectField 7.Sample Form Grid level 8.Default Field Value Example: Species,,TRUE,optional,SelectField,"Atropa belladonna, ...",Sample Description, My question is: What is the 3rd comma separated value on the line used for? In the example what does the value TRUE represent? Thanks, Natalie

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The underlying communication of Galaxy user and server
by Zhe Chen 23 Sep '10

23 Sep '10

Hi, Can you tell me the exact underlying communication of Galaxy? Are they all html POST and GET? What is the format of data send to server and result send back to client? BTW, looks like all the data are stored on the server and never be deleted, why? If too many users are using the server, it may cause a problem. Thanks

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Dataset Id in UCSC link?
by Jesse Erdmann 22 Sep '10

22 Sep '10

In the existing galaxy-central tool XML scripts and the wiki reading I've done I haven't figured out how to get the dataset ID to be used in the hgt.customText URL that will load a particular dataset as a custom track. From http://bitbucket.org/galaxy/galaxy-central/wiki/ExternalDisplayApplications… it looks like I would do something like ${my_dataset.qp}, but Cheetah doesn't like that. I'm going off of the URL used as a link from a BED file to the UCSC Genome Browser as follows (ignore the localhost:8081 bit) and just need to fill in the id bit. http%3A%2F%2Flocalhost%3A8081%2Froot%2Fdisplay_as%3Fid%3D1492%26display_app%3Ducsc%26authz_method%3Ddisplay_at. Essentially I'm outputting an HTML file with links to each interval in a file and want to display it at UCSC. -- Jesse Erdmann Bioinformatics Analyst Masonic Cancer Center University of Minnesota jerdmann(a)umn.edu 612-626-3123 jesse(a)jesseerdmann.com Twitter: http://twitter.com/jesseerdmann

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output name
by Andreu Alibés 22 Sep '10

22 Sep '10

Hi, I'm trying to add to Galaxy a tool that, basically, it runs this way mytool inputfile -outputname=result -outputformat=zzz This would output a file called result.zzz How do I catch the result.zzz file? Because <outputs> <data format="zzz" name="output" /> </outputs> will look for a file called output, but not a file called output.zzz Thanks, Andreu -- -------------------------------------------- Andreu Alibés, PhD Bioinformatics Core & EMBL-CRG Systems Biology Unit Center for Genomic Regulation C/ Dr. Aiguader 88, 08003 Barcelona, Spain Phone: +34 93 316 0202 http://sites.google.com/site/aalibes

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URL in universe_wsgi.ini
by Erick Antezana 21 Sep '10

21 Sep '10

Hi, the following URL (found in the universe_wsgi.ini): http://bitbucket.org/galaxy/galaxy-central/wiki/Config/LoadBalancing , which actually shows an empty page, should be changed to: http://bitbucket.org/galaxy/galaxy-central/wiki/Config/WebApplicationScaling thanks, Erick

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