[galaxy-dev] Multicore

2013-03-26 Thread Alexander Kurze
Hi there, we have a 32 core server but I realised that a lot of programs are only using a fraction of that. I was able to adjust bowtie, bowtie2 and Tophat to use all of the cores but couldn't find an thread/core option for Macs14, Macs2 or PeakRanger. Does anyone know if these programs are

[galaxy-dev] Manage Local data

2013-03-26 Thread Shaun Webb
Hi I am trying to load the mm10 genome and indexes using the manage local data admin feature. The genome downloads ok and so do the liftOver chain files, however the main controller and indexing jobs fail. They just display error, is there any way I can find out more about what is

Re: [galaxy-dev] Multicore

2013-03-26 Thread Quang Trinh
Hi Alexander, There is a -t for PeakRanger to indicate the number of threads. I don't think macs14 or macs2 can run on mutltiple cores - I am cc'ing Tao Lui, the author of macs, who can confirm this. Thanks, Q On Tue, Mar 26, 2013 at 6:15 AM, Alexander Kurze alexander.ku...@gmail.com wrote:

Re: [galaxy-dev] Exporting histories fails: no space left on device

2013-03-26 Thread Joachim Jacob | VIB |
Hi Gordon, Thanks for your assistance and the recommendations. Freezing postgres sounds like hell to me :-) abrt was filling the root directory indeed. So disabled it. I have done some exporting tests, and the behaviour is not consistent. 1. *size*: in general, it worked out for smaller

Re: [galaxy-dev] redirection vulnerability via URL injection

2013-03-26 Thread Vipin TS
Thanks Dan! I am not sure about the dataset redirecting places other than ucsc and wormbase genome browser. By now, this can be done through Trackster right? Then I will probably disable the external redirecting. any comments/suggestions. thanks, --/Vipin Hi Vipin, Thank you for reporting

[galaxy-dev] hello Newbie questions about galaxy and clustering

2013-03-26 Thread Jennifer Jackson
Hello Jereme, I am going to post your question over to the galaxy-...@bx.psu.edu mailing list to give it better visibility to the development community. This is also where you will want to post future questions about your local install. http://wiki.galaxyproject.org/MailingLists For you

Re: [galaxy-dev] Exporting histories fails: no space left on device

2013-03-26 Thread Assaf Gordon
Hello Joachim, Joachim Jacob | VIB | wrote, On 03/26/2013 10:01 AM: abrt was filling the root directory indeed. So disabled it. I have done some exporting tests, and the behaviour is not consistent. 1. *size*: in general, it worked out for smaller datasets, and usually crashed on

Re: [galaxy-dev] galaxy not picking up updates from test toolshed

2013-03-26 Thread Dave Bouvier
Jorrit, Just to eliminate one possible cause of this behavior, could you confirm that your local Galaxy instance's universe_wsgi.ini file's enable_tool_shed_check setting is uncommented and set to True, and the hours_between_check is also uncommented and set to a value between 1 and 12?

Re: [galaxy-dev] galaxy not picking up updates from test toolshed

2013-03-26 Thread jorrit poelen
Hey Dave, Thanks against for your quick response! I checked my universe_wsgi.ini file and can confirm that the enabled_tool_shed_check was *commented*. I've uncommented the settings and changed them to: enable_tool_shed_check = True hours_between_check = 1 Then I followed the steps outlined

[galaxy-dev] best practice to replace the hashing for galaxy-user passwords

2013-03-26 Thread Vipin TS
Dear dev-team, I am interested to implement the secure hashed password specifically SHA-256 or greater to the galaxy users using publicly available python module PBKDF2. I have a piece of python code which will do the job but not quite sure how I can integrate this to my local galaxy code

Re: [galaxy-dev] galaxy not picking up updates from test toolshed

2013-03-26 Thread Dave Bouvier
Jorrit, First, allow me to clarify a point of naming: It's not quite right to say tools in this situation, as tools are only one of several utilities that a tool shed repository can contain, along with datatypes, workflows, repository dependencies, and so on. This is an important

Re: [galaxy-dev] Multicore

2013-03-26 Thread Alexander Kurze
Thanks a lot for your answers. I tried to set the -t value to 32 in peakranger but nothing really happens...it still runs on 1 thread even so it says -t 32 in the execution line I guess I need to contact the author. Thanks for your help! Alex On Tue, Mar 26, 2013 at 2:01 PM, Peter Cock