Re: [galaxy-dev] Populating tool select menu with database data?
Hello Hans-Rudolf, Do you know if the 'dynamic_options' attribute also works for control elements other then select menu's? For example I want to present the user a set of checkboxes that correspond to column names from a file, could I use something like a loop that either iterates on data received from the 'dynamics_option' function or from a meta attribute? To get a bit further off topic, I made a new tabular datatype that has a meta-attribute for storing column names, but I can't use them in my XML files.. Any ideas would be welcome! Regards, Marcel -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu on behalf of Hans-Rudolf Hotz Sent: Tue 2/8/2011 10:04 AM To: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Populating tool select menu with database data? Leandro we use the dynamic_options attribute, eg: inputs param name=foo type=select label=what help=Use tickboxes to select display=radio dynamic_options=ds_fooOptions()/ /inputs outputs data format=fasta name=output label=more foo / /outputs code file=extra_code_for_foo_list.py / help /help /tool and then we have a little python script (extra_code_for_foo_list.py) with the ds_fooOptions function, eg def ds_fooOptions(): List available foos as tuples of (displayName,value) foos = whatever python code is required to generate the tuples return foos I hope this helps, Hans On 02/08/2011 08:32 AM, Leandro Hermida wrote: Hi Dannon, Sorry that I didn't explain well I have a local database with certain information and I would like to dynamically populate a Galaxy tool select menu with the results of a SQL statement. Is this possible? best, Leandro On Mon, Feb 7, 2011 at 6:05 PM, Dannon Bakerdannonba...@me.com wrote: Leandro, Could you elaborate on what you're trying to do, perhaps what database data you're referring to? -Dannon On Feb 7, 2011, at 11:58 AM, Leandro Hermida wrote: Sorry to bug again, Does anyone know where I can find an example on how to dynamically populate a tool select menu with database data? regards, Leandro On Thu, Feb 3, 2011 at 3:32 PM, Leandro Hermida soft...@leandrohermida.com wrote: Hi, Sorry I tried to search for this and couldn't find an example to this basic question where can I find an example on how to populate a tool select menu with database data? best, Leandro ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message. ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Re: [galaxy-dev] Galaxy integration with LSF: seg fault: update
My thanks as well, since we don't really have a way to debug LSF here. Platform only granted us a 1 month license for the development, so I'd have to get another license to debug it. --nate Leandro Hermida wrote: Hi Marina, Thanks for posting updates and information... we've moved from SGE to LSF and are going to implement Galaxy LSF integration next month so what you have posted is very interesting -Leandro On Mon, Feb 7, 2011 at 6:22 PM, Marina Gourtovaia m...@sanger.ac.uk wrote: This has now been narrowed down to a seq fault in the drmaa libraries immediately after submitting a job when an LSF queue is set explicitly with the LSB_DEFAULTQUEUE global variable. Marina On 02/02/2011 16:43, Marina Gourtovaia wrote: Hello I've set up Galaxy to use LSF. My first job has failed because Galaxy submitted it to the default queue, which was wrong in my case. However, Galaxy gracefully survived the failure, I was able to get the job number from the console output and figure out what went wrong. Next time I run the Galaxy with the LSB_DEFAULTQUEUE env variable set like this: LSB_DEFAULTQUEUE=test DRMAA_LIBRARY_PATH=/usr/local/lsf/7.0/linux2.6-glibc2.3-x86_64/lib/libdrmaa.so.1.0.4 PATH=/usr/bin:/software/solexa/bin:$PATH sh run.sh The job is submitted to the correct queue and at this point Galaxy fails with this error: run.sh: line 46: 6506 Segmentation fault python ./scripts/paster.py serve universe_wsgi.ini $@ The job successfully completes in its own time. When I try to run Galaxy again I get the following: galaxy.jobs DEBUG 2011-02-02 16:27:32,565 dispatching job 36 to drmaa runner galaxy.jobs INFO 2011-02-02 16:27:32,675 job 36 dispatched galaxy.jobs.runners.drmaa DEBUG 2011-02-02 16:27:33,192 (36) submitting file /nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/database/pbs/galaxy_36.sh galaxy.jobs.runners.drmaa DEBUG 2011-02-02 16:27:33,192 (36) command is: java -jar /nfs/users/nfs_m/mg8/mygalaxy/galaxy-dist/tool-data/shared/jars/SamToFastq.jar VALIDATION_STRINGENCY=SILENT QUIET=true INPUT=/lustre/scratch103/sanger/mg8/galaxy/datasets/000/dataset_16.dat FASTQ=/lustre/scratch103/sanger/mg8/galaxy/datasets/000/dataset_51.dat SECOND_END_FASTQ=/lustre/scratch103/sanger/mg8/galaxy/datasets/000/dataset_52.dat Job 855341 is submitted to queue test. run.sh: line 46: 6506 Segmentation fault python ./scripts/paster.py serve universe_wsgi.ini $@ ie looks like Galaxy is trying to pick up where it has left and fails again. I configured my job runners like this: start_job_runners = drmaa default_cluster_job_runner = drmaa:/// Any suggestions? Regards Marina -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
[galaxy-dev] Installation Issue on Centos/python 2.4
Trying to install a local copy of Galaxy for evaluation. Downloaded the stable version using: hg clone https://bitbucket.org/galaxy/galaxy-dist I am installing it on a Centos 5 x86_64 Linux kernel which has python 2.4.3 installed. When running sh setup.sh the installation stops with an error building the python_daemon egg. In checking, it is trying to download/build python_daemon 1.5.5 (specified in the eggs.ini). This version of python_daemon uses syntax that depends on python = 2.5. Your README indicates Galaxy requires Python 2.4, 2.5 or 2.6. To check your python version, run: ... Does Galaxy still run under python 2.4? (PS: I have lots of Linux/Perl experience, but virtually no python expertise.) Thanks //=\John Powell, CAPT, Ret. USPHS Phone: (301) 496-2963 \=//Building 12A, Room 2033FAX: (301) 402-2867 //=\ National Institutes of Health \=// Bethesda, MD 20892-5624Work: j...@helix.nih.gov //=\ Personal: jpow...@erols.com \=// //=\ BioInformatics Molecular Analysis Section-BIMAS/CBEL/CIT/NIH - ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
