Re: [galaxy-dev] Galaxy Main Server Tool Repository

2012-02-08 Thread Li Charlie Xia
Thanks for replying. I will check the them out. On Tue, Feb 7, 2012 at 5:31 AM, Nate Coraor wrote: > Hi Charlie, > > Just a minor correction, the Main server is Solaris 10, the clusters on > which jobs run are Debian testing/unstable and RHEL 5.7. > > --nate > > On Feb 6, 2012, at 9:01 PM, Danno

Re: [galaxy-dev] Error when attempting to get_updates from toolshed

2012-02-08 Thread Greg Von Kuster
This is fixed in change set revision 6691:c9bdeba75bd1 on our central repo. Thanks very much for reporting this. Greg On Feb 7, 2012, at 7:40 PM, Ira Cooke wrote: > Dear Greg, > > In the latest version of the galaxy-central code there seems to be a bug > preventing me from updating my tools

Re: [galaxy-dev] Garli and Tandem Repeats Finder wrappers

2012-02-08 Thread Jennifer Jackson
Hello Alex, Both of these tools are in the Tool Shed. An easy way to locate these (and to search for tools/wrappers related to Galaxy in general) is: http://galaxy.psu.edu/search/getgalaxy/ More about the Tool shed: http://wiki.g2.bx.psu.edu/Tool%20Shed More about the searches: http://wiki.g2

Re: [galaxy-dev] set_metadata.py

2012-02-08 Thread Nate Coraor
On Feb 7, 2012, at 11:25 AM, Bram Slabbinck wrote: > Hi > > I am running into a problem with the scripts/set_metadata.py file since > the last update of galaxy-dist. In this script the name of the universe > file is hard-coded as 'universe_wsgi.ini', see line 44: > > config_file_name = 'universe

Re: [galaxy-dev] Problems with custom data types and sniffers in shed tools

2012-02-08 Thread Greg Von Kuster
Proprietary datatypes are loaded before datatypes in the distribution as of change set revision 6693:865d998a693d, which is available in our central repo. Proprietary datatypes contained in installed repositories are loaded in order of oldest installation first, followed by next olderst install

Re: [galaxy-dev] Problems with custom data types and sniffers in shed tools

2012-02-08 Thread Greg Von Kuster
To clarify, proprietary datatypes currently being loaded will be ignored if they conflict with a proprietary datatypes that was already loaded. Only datatypes defined in the datatypes_conf.xml file will take precedence, and override conflicts. On Feb 8, 2012, at 11:34 AM, Greg Von Kuster wrote

Re: [galaxy-dev] Status on importing BAM file into Library does not update

2012-02-08 Thread Ryan Golhar
Hi Nate - I finally got a chance to look at this briefly, but I must admit, my Python skills are lacking. In the Bam class in binary.py, all I see are calls to proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=open( stderr_name, 'wb' ) ) which, to me, look like calls to exec

Re: [galaxy-dev] Garli and Tandem Repeats Finder wrappers

2012-02-08 Thread Oleksandr Moskalenko
On Feb 8, 2012, at 10:07 AM, Jennifer Jackson wrote: > Hello Alex, > > Both of these tools are in the Tool Shed. An easy way to locate these (and to > search for tools/wrappers related to Galaxy in general) is: > http://galaxy.psu.edu/search/getgalaxy/ > > More about the Tool shed: > http://wi

Re: [galaxy-dev] Problems with custom data types and sniffers in shed tools

2012-02-08 Thread Greg Von Kuster
In revision 6695:c06d7cef9125 I simplified the precedence rules. A datatypes currently being loaded will always replace a conflicting datatype that was previously loaded. This same behavior applies to datatype sniffers (sniffers loaded later will replace sniffers loaded previously), but will b

Re: [galaxy-dev] Status on importing BAM file into Library does not update

2012-02-08 Thread Fields, Christopher J
'samtools sort' seems to be running on our server end as well (not on the cluster). I may look into it a bit more myself. Snapshot of top off our server (you can see our local runner as well): PID USER PR NI VIRT RES SHR S %CPU %MEMTIME+ COMMAND 3950 galaxy20

Re: [galaxy-dev] Status on importing BAM file into Library does not update

2012-02-08 Thread Fields, Christopher J
Forgot to add, but this also seems tied to the same problem Ryan's describing. IIRC Galaxy also runs 'samtools sort' after certain jobs, correct? chris On Feb 8, 2012, at 8:32 PM, Fields, Christopher J wrote: > 'samtools sort' seems to be running on our server end as well (not on the > cluste