- galaxy-dev - lists.galaxyproject.org

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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Re: [galaxy-dev] [galaxy-user] plugging R into galaxy
by Peter 12 Nov '10

12 Nov '10

On Fri, Nov 12, 2010 at 1:09 PM, Anthony Ferrari <ferraria(a)gmail.com> wrote: > OK. I have made some tests this morning to figure this all out. > Indeed, the problem with ">" is that it catches every single message R sends > to STDOUT and not only object of your interest, so this is definitely not a > reliable solution. Solution suggests by Alex worked perfectly well. > I would suggest also to use the 'trailingOnly=TRUE' option within the > commandArgs() call in the R script. That allows you to only care about the > args given after the '--args' option. You can then forget how many previous > options you have in your command line (--vanilla, --slave, -f or others...). > First parameter useful to your R script would then be > commandArgs(trailingOnly=T)[1] and so on. That is a very handy tip, commandArgs(trailingOnly=T), thanks! > There is just another little point that I would like to clarify. At the > beginning my tests didn't work at all and I realize that I have to give the > full path to the R script (in the command tag) to make it work. What happens if you do <command> rather than <command interpreter="bash">? Peter P.S. Cross posted to Galaxy-dev, could we continue this there?

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Dataset search suggestion
by SHAUN WEBB 12 Nov '10

12 Nov '10

I now have a large number of datasets saved under my account and it is difficult to find previous datasets that I need for new histories. It would be useful to be able to search by history name,tags,annotation in the advanced set. I tend to add tags and meaningful names to each history but it is rather tedious to annotate and tag every dataset. Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Getting problem while executing program by using DRMAA_PYTHON package
by hari krishna 12 Nov '10

12 Nov '10

This is my program example.py .... when i trying to execute this code am getting error as shown below.... can u please help anything for proceeding further.... my python version is 2.4 and ctype that i installed is pygame-ctypes-0.09... #!/usr/bin/env python import drmaa def main(): """Create a drmaa session and exit""" s=drmaa.Session() s.initialize() print 'A session was started successfully' s.exit() if __name__=='__main__': main() ~ [gridmon@g8 DRMAA]$ python example.pyc Traceback (most recent call last): File "example.py", line 3, in ? import drmaa ImportError: No module named drmaa [gridmon@g8 DRMAA]$ cd drmaa-0.4b3 [gridmon@g8 drmaa-0.4b3]$ python example.pyc Traceback (most recent call last): File "example.py", line 3, in ? import drmaa File "/home/gridmon/DRMAA/drmaa-0.4b3/drmaa/__init__.py", line 30, in ? import ctypes as _ct ImportError: No module named ctypes -- Thanks & Regards, Hari Krishna .M

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