Re: [galaxy-dev] Build the Galaxy under Cluster

2013-07-31 Thread shenwiyn
Hi Carlos, Thank you very much for your help.I use Galaxy with the torque2.5.0,pbs_python for a test.It seems to work successfully ! shenwiyn From: Carlos Borroto Date: 2013-07-10 01:49 To: shenwiyn CC: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Build the Galaxy under Cluster Hi

[galaxy-dev] shall us specify which tool run in cluster?

2013-07-31 Thread shenwiyn
Hi Thon Deboer , I am a newer in Galaxy.I installed my Galaxy with Torque2.5.0 ,and Galaxy uses the pbs_modoule to interface with TORQUE.But I have some question of the job_conf.xml : 1.)In your job_conf.xml ,you use regularjobs,longjobs,shortjobs...to run different jobs ,how our Galaxy know

Re: [galaxy-dev] shall us specify which tool run in cluster?

2013-07-31 Thread Ido Tamir
On Jul 31, 2013, at 8:52 AM, shenwiyn shenw...@gmail.com wrote: Hi Thon Deboer , I am a newer in Galaxy.I installed my Galaxy with Torque2.5.0 ,and Galaxy uses the pbs_modoule to interface with TORQUE.But I have some question of the job_conf.xml : 1.)In your job_conf.xml ,you use

[galaxy-dev] Mail is not configured for this Galaxy instance.

2013-07-31 Thread shenwiyn
Hi everyone, In my local Galaxy,when I want to reset my Login password,some error occurre :Mail is not configured for this Galaxy instance. Please contact an administrator. Could anyone tell me some imformation about how to configure the mail for my Galaxy instance? Thank you very much.

Re: [galaxy-dev] Mail is not configured for this Galaxy instance.

2013-07-31 Thread Hans-Rudolf Hotz
Hi Shenwiyn You need to specify a SMTP server. Have a look at the 'smtp_server' settings in your universe_wsgi.ini file. Regards, Hans-Rudolf On 07/31/2013 04:19 PM, shenwiyn wrote: Hi everyone, In my local Galaxy,when I want to reset my Login password,some error occurre :Mail is not

[galaxy-dev] Velvet optimizer problems : Urgent help.

2013-07-31 Thread Perez, Ricardo
Dear all, When trying to run velvet optimizer in galaxy, all the files we get return the following: No peek When looking at the output of galaxy, we get the following: galaxy.jobs.runners.local DEBUG 2013-07-31 09:31:46,829 execution finished: perl

[galaxy-dev] reference genomes missing

2013-07-31 Thread Gerald Bothe
I installed a local instance of GALAXY following the instructions at Get Galaxy ... in the Wiki. It installed ok, but when I tried the Bowtie2 mapper with a test data set, I noticed that the reference genomes are missing. How can I get the reference genomes (e.g. latest version of mouse and

[galaxy-dev] August 2013 Galaxy Update Newsletter is out

2013-07-31 Thread Dave Clements
Hello all, The August 2013 Galaxy Update is now availablehttp://wiki.galaxyproject.org/GalaxyUpdates/2013_08 . *Highlights:* - *GCC2013 Reporthttp://wiki.galaxyproject.org/GalaxyUpdates/2013_08#GCC2013_Report :* Meeting summaries, and links to videos, talks, posters, and Training

[galaxy-dev] Choosing which nodes to run on for a whole history (Galaxy cluster)

2013-07-31 Thread Ben Gift
I'm setting up Galaxy and Torque with my cluster and I was wondering if I could set it up so that nodes could be assigned for a whole history. This way I can re-run histories on certain nodes for benchmarking runtimes. It seems that the closest I can get with the built in functionality is

[galaxy-dev] Problems with sharing datasets

2013-07-31 Thread Ricardo Perez
Dear all, When trying to share a dataset in galaxy among users, usually this sharing fails. Usually when we go to Dataset Securities and try to change the permissions of the datasets the sharing fails. Instead, it keeps the original configuration and then it will open another galaxy page inside

Re: [galaxy-dev] Velvet optimizer problems : Urgent help.

2013-07-31 Thread Ricardo Perez
On 07/31/2013 11:24 AM, Perez, Ricardo wrote: Dear all, When trying to run velvet optimizer in galaxy, all the files we get return the following: No peek When looking at the output of galaxy, we get the following: galaxy.jobs.runners.local DEBUG 2013-07-31 09:31:46,829 execution finished:

[galaxy-dev] importing data from other public websites into galaxy

2013-07-31 Thread Prasun Dutta
Hi, I wish to import data into my local instance of galaxy from another website. Kindly let me know how to achieve that and what all is required. I want to import data from a chemoinformatic database (mainly compound structures) into galaxy and run my own analysis tools on them.  Regards,

[galaxy-dev] enable to edit pages

2013-07-31 Thread Philipe Moncuquet
Hi guys, Since the last update of Galaxy. We are enable to edit pages on our local instance. Pages can be viewed without problems but not editing. The server error we get is as foolow, any advice would be greatly appreciated. URL:

[galaxy-dev] job_conf.xml questions

2013-07-31 Thread shenwiyn
Hi Ido Tamir, I have the same question too. I set megablast as long_jobs for the test,when I cancel my megablast job in Galaxy history before it finishs,it still work in my background.The drmaa_external_killer.py seems doesn't work.I don't know where is the problem,and hope someone can help me