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

visualization tool
by shashi shekhar 23 Aug '11

23 Aug '11

Hi All, I want to add my own Visualization tool in local instance of galaxy .how i will do it in galaxy ? i want to integrate jmol in galaxy. Regards shashi

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Boolean options in toolconfigs: yes/no vs. give/omit flag.
by Samuel Lampa 23 Aug '11

23 Aug '11

Hi, I'm trying to parse the XML toolconfig format, for generating a lightweight command config wizard in an Eclipse based product. I wonder: Boolean parameters for some tools (such as the emboss/textsearch one), seems to allow always giving the parameter's flag at all times, and just change the following value between "yes" and "no" for these params, like: textsearch -caseinsensitive yes or textsearch -caseinsensitive no On the other hand, I guess there are many tools which tell such boolean options just by giving the flag itself, so it would by analogy be: textsearch -caseinsensitive or textsearch My question is, how can I see the difference between these two cases, in the tool config file? (Unfortunately I don't know any of the wrapped tools good enough to know where to look for a flag of the latter kind). Cheers // Samuel -- System Expert / Bioinformatician SNIC-UPPMAX HPC Center Uppsala University, Sweden -------------------------------------- E-mail: samuel.lampa(a)scilifelab.uu.se Phone: +46 (0)18 - 471 1060 WWW: http://www.uppmax.uu.se Uppnex: https://www.uppnex.uu.se

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Fwd: [SOLVED] Re: DRMAA broken following SGE update. How to fix?
by Roman Valls 23 Aug '11

23 Aug '11

I'm glad it worked Chris, I'm keeping thread on the mailing list for future reference... -------- Original Message -------- Subject: Re: [galaxy-dev] DRMAA broken following SGE update. How to fix? Date: Tue, 23 Aug 2011 11:56:13 +0100 From: Chris Cole <chris(a)compbio.dundee.ac.uk> Organization: University of Dundee To: Roman Valls <brainstorm(a)nopcode.org> Hi, The SGE_ROOT variable was the same as always, but it turns out I had a DRMAA_LIBRARY_PATH path that was still pointing to the old path. It's such a long time since I set up galaxy that I'd forgotten about it. Changed it and Galaxy is working again. Thanks to you and Remy for pointing me in the right direction. Chris On 23/08/11 09:32, Roman Valls wrote: > Did you adjust the SGE_ROOT environment variable to point to the > libdrmaa for SGE (probably /opt/sge_62u5_gr/bin/lx24-amd64) ? > > This is of course just a guess, could you please provide some error > messages/logs ? > > Cheers, > Roman > > On 2011-08-23 10:20, Chris Cole wrote: >> BUMP >> >> Does anyone have any idea on this? Our Galaxy is currently out of action >> until this is sorted. >> Thanks, >> >> Chris >> >> On 22/08/11 10:08, Chris Cole wrote: >>> Hi, >>> >>> Following a recent update to our SGE, DRMAA is failing to load in >>> galaxy. The reason being that the path has changed. How do I change the >>> path for galaxy to find the libdrmaa module? >>> Cheers, >>> >>> Chris >>> >>> >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> >> http://lists.bx.psu.edu/ > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/

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Brad's GFF parser in a Biopython repository
by Peter Cock 23 Aug '11

23 Aug '11

Hi Brad, I managed to do a git script to select out the GFF code and tests from your bcbb repository and get it into the Biopython source tree. The folder changes made it interesting ;) Input: https://github.com/chapmanb/bcbb (master branch) Output: https://github.com/peterjc/biopython/tree/brad_gff The tests pass, but that is as far as I have got with this. Brad, could you have a look at this new branch for sanity checking please? Peter

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DRMAA broken following SGE update. How to fix?
by Chris Cole 23 Aug '11

23 Aug '11

Hi, Following a recent update to our SGE, DRMAA is failing to load in galaxy. The reason being that the path has changed. How do I change the path for galaxy to find the libdrmaa module? Cheers, Chris -- Dr Chris Cole Senior Research Associate (Bioinformatics) College of Life Sciences University of Dundee Dow Street Dundee DD1 5EH Scotland, UK url: http://network.nature.com/profile/drchriscole e-mail: chris(a)compbio.dundee.ac.uk Tel: +44 (0)1382 388 721 The University of Dundee is a registered Scottish charity, No: SC015096

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Tool Config Syntax Wiki page, <actions> tag
by Peter Cock 22 Aug '11

22 Aug '11

Hi, There seems to be something wrong with the <actions> tag on the wiki page: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax If doesn't appear in the table of contents, and there are three curly brackets after the section name: <actions>}}} Peter

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problem with build_chrom_db.py
by Curt Palm 22 Aug '11

22 Aug '11

I've been configuring my local instance of galaxy to use trackster according to the instructions on https://bitbucket.org/galaxy/galaxy-central/wiki/Visualization when I run the script: python ./cron/build_chrom_db.py ./tool-data/shared/ucsc/chrom/ I get files that begin with: <META http-equiv="Content-Script-Type" content="text/javascript"> chr1 247249719 chr1_random 166326 ... this causes an error in the browser: "Could not load chroms for this dbkey:" if i delete the first line " <META http-equiv="Content-Script-Type" content="text/javascript">" from the .len file, then trackster works fine. I'm thinking there is a new line the input to build_chrom_db.py that is not getting stripped by this script thanks, Curt Palm ******************************************************* Curtis J. Palm cpalm(a)stanford.edu Stanford Genome Technology Center MC: 8307 office: 650-812-1994 cell: 408 858-7849 *******************************************************

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upload.py fails with files having commas in file name
by Chorny, Ilya 22 Aug '11

22 Aug '11

The ftp upload module fails when a file has a comma in the file name for example test.bam works but when copied to test,test.bam that file fails. Cheers, Ilya Ilya Chorny Ph.D. Bioinformatics - Intern ichorny(a)illumina.com<mailto:ichorny@illumina.com> 858-202-4582

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Re: [galaxy-dev] Adding Libraries
by Nate Coraor 22 Aug '11

22 Aug '11

Tanguy LE CARROUR wrote: > Dear Nate! > > On Wed, 2010-09-01 at 17:21 +0200, Tanguy Le Carrour wrote: > > On Wed, 2010-09-01 at 11:14 -0400, Nate Coraor wrote: > > > This would be a great case for use of the (experimental) API. Set > > > 'enable_api = True' in the config and then have a look at the > > > README/scripts in scripts/api/ > > > > Thanks! It looks great! I'll test this. > Unfortunately I've had no time those last weeks... months to play with > Galaxy API! > I've just downloaded the latest Galaxy version and I'm happily starting > to test it! > The Sample Tracking features are just great! Especially the "External > services" importer which I planed to use to access our data repository. > > But... after installing the rabbitMQ stuff (was it really necessary to > rely on MQ?) I tried to import data and after one day it's still "In > queue". There is no obvious error message in the logs... > Is the feature still in testing or is it supposed to be production > ready? Hi Tanguy, It's under pretty heavy development and there are some major changes planned. Part of this will be dropping rabbitMQ (or at least the requirement for rabbitMQ - we will probably retain AMQP in the form of a slower python-based MQ that can be supplanted with rabbitMQ). That said, rabbitMQ should only be required for the barcode scanning functionality. For datast transfer, see the Transfer Manager and Deferred Job Runner, enabled with 'enable_beta_job_managers = True' in the config. > I would really love being able to use it... it would be even better with > a "Link instead of copying"... but as it seems to use SCP I guess it's > not possible! Yes, you won't be able to link instead of copying using this method. It could be extended to do so but for now, it assumes it is copying data from a remote service. > Just to give you an overview of what we would like to do... > We already have a project management system that also handles the raw > data. We would need a workflow manager to work with the data (that are > on the same drive). Somehow importing through the "Data Library" is a > pain. With the external services the sample-file link is easy to > create... but the data are copied! > > I guess there would be a solution using the API but went I tried it it > was still in beta phase. It's still in beta but it should definitely do what you're trying to do. --nate > > Any idea/advice welcome! > > Thanks again for all your good work! > > Best regards, > Tanguy > > -- > Tanguy LE CARROUR > > Functional Genomics Center Zurich > ETH Zurich / University of Zurich > Winterthurerstrasse 190 > 8057 Zurich > Switzerland > >

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regarding updating data libraries
by Sridhar A Malkaram 22 Aug '11

22 Aug '11

Hi, I was wondering if there is a method of updating datasets in a data library, which was created using the option, "Upload files from filesystem paths" and selecting "Link to files without copying into Galaxy". An update operation should reflect any changes that occurred in the filesystem path. Is it possible? Additionally a useful feature would be to have a search option in the data library and current history panels, similar to the one in the tool-box. When the data library is very large (for example, when a big filesystem is imported into galaxy), the search feature will facilitate easy location of files. Thank you, Sridhar

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