Re: [galaxy-dev] Information about server availability
Hi, I want to stop receiving emails to this account(bas...@gmail.com), and want to use another email for galaxy developers list. How can I replace this email account with another? Thanks, Basam. On Thu, Jan 5, 2012 at 10:52 AM, sarah Maman sma...@toulouse.inra.frwrote: Dear all, I would like to get the latest copy from the repository ( https://bitbucket.org/galaxy/**galaxy-disthttps://bitbucket.org/galaxy/galaxy-dist) in order to install Galaxy. But, unfortunatly, no server is available to handle this request (503 Service Unavailable). Could you, please, help me ? Do you know when this information will be available ? Please, excuse me if this information is available on your web and if I have not seen it. Happy new year, Sarah Maman -- Sarah Maman INRA - LCG - SIGENAE Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Tax: +33(0)5.61.28.57.53 __**_ 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/
[galaxy-dev] amplicon reads(with errors)
Dear All, Is there a way to generate 454 simulated amplicon reads with errors using galaxy. Happy New Year, Bassam Tork. ___ 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/
Re: [galaxy-dev] defining genome assembler in galaxy
Dear Jeremy, Thank You very much, I will try your suggestion. Could you please guide me to the link/webpage that talks about checking the job manually using top/qstat/similar. Happy New Year, Bassam Tork. On Thu, Dec 29, 2011 at 9:18 AM, Jeremy Goecks jeremy.goe...@emory.eduwrote: My idea was to pass all above including main.bash as parameters to the python wrapper (called run.py, attached), as follows: where the last parameter sys.argv[7] is the output file, specified by xml file. This is the correct approach. But galaxy was running for more than 3 hours, although it should take only 7-10 minutes on our server with no results. Vispa should write its output to dataset_192_I_2_20_CNTGS_DIST0_EM20.txt , where dataset_192 .txt is the reads file.But dataset_192_I_2_20_CNTGS_DIST0_EM20.txt did not appear in galaxy-dist/database/files/000. run.py: simply coppies data from dataset_192_I_2_20_CNTGS_DIST0_EM20.txt to galaxy output file, but nothing is coppied since dataset_192_I_2_20_CNTGS_DIST0_EM20.txt was not created. How could the results appear?Could somebody help me ? The first thing to check is if run.py functions correctly outside of Galaxy. If so, try checking the job manually using top/qstat/similar system utilities to figure out where the job is stuck. Good luck, J. ___ 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/
[galaxy-dev] defining genome assembler in galaxy
*Hello,*
I am interested in defining vispa tool on galaxy
*(http://alla.cs.gsu.edu/~software/VISPA/vispa.html).*
*we usually run vispa using main.bash file as follows
./main.bash readFile referenceFile threads n t
where:
threads: number of threads
n:number of mismatches
t:mutation rate
the output file name,we are interested in is not passed as parameter,
but its named as follows:
if inupt file name= readFile.fas then output file name is
readFile_I_2_20_CNTGS_DIST0_EM20.txt
('readFile'+'_I_2_20_CNTGS_DIST0_EM20.txt')
*My idea was to pass all above including main.bash as parameters to the
python wrapper (called run.py, attached), as follows:
where the last parameter sys.argv[7] is the output file, specified by xml
file.
But galaxy was running for more than 3 hours, although it should take
only 7-10 minutes on our server with no results.
Vispa should write its output to dataset_192_I_2_20_CNTGS_DIST0_EM20.txt
, where dataset_192 .txt is the reads
file.But dataset_192_I_2_20_CNTGS_DIST0_EM20.txt did not appear in
galaxy-dist/database/files/000.
run.py: simply coppies data from dataset_192_I_2_20_CNTGS_DIST0_EM20.txt
to galaxy output file, but nothing is coppied
since dataset_192_I_2_20_CNTGS_DIST0_EM20.txt was not created.
How could the results appear?Could somebody help me ?
*Your Help Is Highly Appreciated,
Bassam Tork.*
*PhD - GSU*
___
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/
