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

Feature Update: Expanded Reference Genomes for NGS Tools
by Jennifer Jackson 16 Nov '10

16 Nov '10

Feature Update: Expanded Reference Genomes for NGS Tools Expanded genome data is now available on Galaxy's main server http://usegalaxy.org. The expanded genome data are organized into the following categories: Full = All chromosomes (or scaffolds/contigs) released as part of the full build from the data source. Many will also include the latest Mitochondrial chromosome, if available. Full is the default genome build type for all reference genomes and what was previously available. Canonical = All chromosomes released that represent the core chromosomes (including mitochondrial) for that species and build. Canonical will not include chromosomes with names that include: chrUn, chrN_random, chrN_hap_XX (haplotype), and similar. Coming soon will also be the reference genome variants Male and Female. Many genomes will default to Male (identical to Canonical). Female will be the Canonical minus a chrY chromosome. The NGS Tools with expanded genome data available: Bowtie and BWA. Please note that previously used/saved settings will default to "Full". Other NGS Tools are planned to have expanded reference genome data available in the future as appropriate. Reference genomes part of the expanded dataset include: galGal3 hg18 hg19 mm8 mm9 panTro2 rn4 taeGut1 tetNig1 tetNig2 Thanks for using Galaxy! Galaxy team November 16, 2010

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Galaxy/Python and Bioinformatics Engineers positions at the J.Craig Venter Institute
by Krampis, Konstantinos 16 Nov '10

16 Nov '10

Hi all, We have a few open Bioinformatics/Software Engineers positions at the J.Craig Venter Institute, one of which involves largely developing further the Galaxy platform for use in-house (writing additional Galaxy wrappers for internal pipelines / tools, integrating Galaxy with existing cluster systems, SGE etc.) Besides working with Galaxy, these positions involve quite a broad range of software development opportunities (languages ranging from Perl to Java), while at the same time they offer great learning opportunities for working with next- generation sequencing datasets, and learning fundamental techniques related to bioinformatic analysis of these types of data. Please pass the word, feel free to email me for additional information, or even go to the careers page to apply: https://careers.jcvi.org/careers/Careers.aspx?adata=Q%2fhMgU9ioOU2Q2IBMeDlP… many thanks ! -- Konstantinos (Ntino) Krampis, Ph.D. Bioinformatics Engineer J.Craig Venter Institute Cell. 540-200-8277 http://twitter.com/agbiotec

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Running job status not working
by Chris Cole 16 Nov '10

16 Nov '10

Hi, Another problem in the update I've applied. New jobs don't change state in the Galaxy interface, but they are being correctly farmed onto our cluster via DRMAA. THis is the output I get: galaxy.jobs INFO 2010-11-12 16:02:43,029 job 2187 dispatched galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:43,836 (2187) submitting file /homes/www-galaxy/galaxy_devel/database/pbs/galaxy_2187.sh galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:43,836 (2187) command is: perl /homes/www-galaxy/local_tools_devel/bin/get_RNA_align.pl --rna hsa-mir-30a --num-reads 1 --expt smRNAHelaC --format text --order pos --out /homes/www-galaxy/galaxy_devel/database/files/002/dataset_2317.dat --noverbose galaxy.jobs.runners.drmaa INFO 2010-11-12 16:02:43,857 (2187) queued as 989766 galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:44,820 (2187/989766) state change: job is queued and active galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:46,824 (2187/989766) state change: job is running galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:48,121 (2187/989766) state change: process status cannot be determined galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:50,128 (2187/989766) state change: job finished normally galaxy.jobs DEBUG 2010-11-12 16:02:50,530 job 2187 ended If I manually refresh the history panel then the grey history item goes green. Anyone else seen this behaviour? Thanks, Chris

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Re: [galaxy-dev] Hardware and Users
by Matt Vincent 15 Nov '10

15 Nov '10

Hello, We are currently implementing galaxy and were wondering how many users you currently support, the hardware that you use, and the amount of storage (terabytes, petabytes, etc.) you are using. Thanks! Matt

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Output redirect
by Zhe Chen 15 Nov '10

15 Nov '10

Hi, For general galaxy output, I need to define sth like <outputs> <data format="input" name="out_file1" metadata_source="input"/> </outputs> and put $out_file1 as a parameter in the command tag. To my understanding, Galaxy will save the $out_file1 into a file and retrieve and display it on the result panel. I have a *.pl file which takes inputs and generate a file (result.txt) in my local server and return a file path. Can I redirect the galaxy output to this file? Currently, I am reading the file using the file path and push the content in the file into $out_file1. For large files, it is a waste of computing time and resource (since Galaxy will generate another file). Is there a solution for this? Thanks

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searching libraries
by Kimberly Begley 15 Nov '10

15 Nov '10

Hello, I have a rather large library that I would like to be able to search - from the interface I see that I can search only on the top level name and description - is there any functionality to search the contents of a library (mainly the information/desription section) Cheers, Kimberly

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Galaxy Installation on Linux
by Wong Foo Lam 15 Nov '10

15 Nov '10

Dear Support We have users who are using Galaxy and would like to have this application installed on our compute cluster. I read through the documentation for using Galaxy both on a web browser and on a compute cluster. The document states that a qsub command line can be submitted when using on a cluster. Currently the info documented on this weblink: http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster mentions the qsub -I command. Does this mode sets a platform for user to launch the interactive web browser? I am looking at the option of not launching the web browser where we launch the task with an input file and then the output files are appended to a designated folder. Is it possible to know whether Galaxy software can be installed as a standalone without launching a web browser to submit & run sequencing tasks. Or the interactive web browser is a mandatory interface for running this application regardless of local system or on a compute cluster. Looking forward to hearing from you soon. Regards Foo Lam [cid:image001.gif@01CB80BC.219AC830] WONG Foo Lam (Mr) | Senior HPC Application Engineer | High Performance Computing Centre | Nanyang Technological University 50 Nanyang Avenue, North Spine, Block NS4-04-25 Singapore 639798 Tel: (65) 6592 2414 GMT+8h | Email: foo-lam.wong(a)ntu.edu.sg<mailto:foo-lam.wong@ntu.edu.sg> | Web: www.hpc.ntu.edu.sg<http://www.ntu.edu.sg/> ________________________________ CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its content. Thank you. Towards A Sustainable Earth: Print Only When Necessary

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Galaxy wrappers for TMHMM and SignalP
by Peter 15 Nov '10

15 Nov '10

Hello, Are there any existing Galaxy wrappers for the command line tools (or the online services) TMHMM v2.0 (Trans-Membrane Hidden Markov Model) and SignalP v3.0 (Signal Peptide)? http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp Both take protein FASTA files for input, but there are a few extra considerations here like limiting each call to TMHMM to 4000 proteins (IIRC), the possibility to split the job in order to take advantage of multiple cores, and parsing the output into a Galaxy friendly tabular form. Thanks, Peter

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pbs_submit failed, PBS error 15024: Max hop count exceeded
by Grainne Kerr 15 Nov '10

15 Nov '10

Dear all, I'm not sure if its a galaxy issue, but perhaps someone could give me some advice on where to look or some configuration to set or... I am trying to set up a local installation of Galaxy in for a multi-uer environment. I've installed it on a compute cluster, running centos 5.5, python2.4, a TORQUE scheduler with Maui. Server name: b110-sc-hdn Compute cluster has three nodes. These are called: headnode, computenode1, computenode2 The default queue on the cluster is called "galaxy_queue". I've set jobs to run on this queue in the universe_wsgi.ini file However, when I try to run a job, I get the following error: "galaxy.jobs.runners.pbs DEBUG 2010-11-14 16:48:56,410 (59) pbs_submit failed, PBS error 15024: Max hop count exceeded" >From the research I have done, seemingly this occurs when there are issues resolving the domain name. But, I don't know how to check this or fix this. I've ran the attached python test script which imports pbs python package. And it works fine. In the script, if I change the server name to "b110-sc-hdn", I recreate the error. Is there something obvious I am not getting? Any help would be very much appreciated and thanks alot for an exceptional tool! Grainne.

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mysql config problem
by Bossers, Alex 15 Nov '10

15 Nov '10

Hi All, maybe a silly question. I am trying to get galaxy running using a mysql DB behind apache. I followed the wiki instructions on how to setup a production server version. Which covered most (of which most steps seem ok and working as far as I could test). I have troubles with the mysql DB part. Mysql is running ok and the user and pass and DB exist for a system user galaxy. However when I try to start the server (after getting some extra eggs) it fails with something like: ..... snip... File "/opt/galaxy_central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 198, in __init__ self.connection = self.__connect() File "/opt/galaxy_central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py", line 261, in __connect connection = self.__pool._creator() File "/opt/galaxy_central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/strategies.py", line 80, in connect raise exc.DBAPIError.instance(None, None, e) OperationalError: (OperationalError) (1045, "Access denied for user 'galaxy'@'localhost'<mailto:'galaxy'@'localhost'> (using password: NO)") None None So I think its the alchemy connection line.... in the universe_wsgi.ini... and the eroor says password NO....confused. Below what I have now but I guess there is something wrong... tried many but failed. The alchemy docs didn't help me either :( database_connection = mysql:///galaxy:password_here@localhost/galaxy?unix_socket=/var/run/mysqld/mysqld.sock I also tried putting the user and DB info separate using and alternative line while removing that info from the line stated above; mysql_db = mysql://galaxy:password_here@localhost/galaxy No luck either Thanks Alex

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