- galaxy-dev - lists.galaxyproject.org

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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Galaxy Cluster Configuration
by Christoph Ruttkies 22 Aug '11

22 Aug '11

Dear Galaxy-Dev Team, I have a problem concerning the integration of galaxy into a cluster environment. Galaxy is installed on a server that has access to the local cluster network and is configured as a submit host for the Sun Grid Engine running on the cluster nodes. So it is configured to use drmaa to submit its jobs. Everytime submitting a job from the galaxy webfrontent the qmaster daemon on the sge-admin host dies with the message !!!!!!!!!! got NULL element for SME_message_list !!!!!!!!!! in the logs. The SGE version is 6.2. Submitting jobs from the command-line with qsub is working without any problems. Do you have any idea? Best regards, Christoph

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When writing wrapper do not use shutil.copy()
by Chorny, Ilya 19 Aug '11

19 Aug '11

If possible when writing wrappers do not use shutil.copy() when copying a file to a dataset_(job_id).dat file. shutil.copy() tries to change the permission of the copied to file. Better to use shutil.copyfile(). Ilya Chorny Ph.D. Bioinformatics - Intern ichorny(a)illumina.com<mailto:ichorny@illumina.com> 858-202-4582

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trackster problem with IE8 and IE7 when using "June 23, 2011" release
by Hans-Rudolf Hotz 19 Aug '11

19 Aug '11

Hi I am sorry to be a pain in the neck, but as part of our quarterly upgrade procedure, I am stumbling across the next problem: Can anybody confirm, that the visualization does not work with the "June 23, 2011" release (changeset: 5743:720455407d1c) when using IE8 or IE7 on windows XP? (it works with chrome and firefox6 on windows XP, and no problems with mac and linux) And like the previous problems, is there a quick fix available? Thank you very much for your help Regards, Hans

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Problems with Galaxy on a mapped drive
by Peter Cock 19 Aug '11

19 Aug '11

Hi all, In my recent email I mentioned problems with our setup and mapped drives. I am running a test Galaxy on a server under a CIFS mapped drive. If I map the drive with noperms then things seem to work with submitting jobs to the cluster etc, but that doesn't seem secure at all. Mounting with strict permissions seems to cause various network latency related problems in Galaxy though. Specifically during loading the converters and history export tool, Galaxy creates a temporary XML file which it then tries to parse. I was able to resolve this by switching from tempfile.TemporaryFile to tempfile.mkstemp and adding a 1s sleep, but it isn't very elegant. Couldn't you use a StringIO handle instead? Later during start up there were two errors with a similar issue - Galaxy creates a temp folder then immediately tries to write a tar ball or zip file to it. Again, adding a 1 second sleep after creating the directory before using it seems to work. See lib/galaxy/web/controllers/dataset.py After that Galaxy started, but still gives problems - like the issue reported here which Galaxy handled badly (see patch): http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-July/006213.html Here again, inserting a one second sleep between writing the cluster script file and setting its permissions made it work. If those are the only issues, that can be dealt with. But are there likely to be lots more similar problems of this nature later on? That is my worry. How are most people setting up mapped drives for Galaxy with a cluster? Thanks, Peter

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