Thanks for replying. I will check the them out.
On Tue, Feb 7, 2012 at 5:31 AM, Nate Coraor n...@bx.psu.edu 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
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.
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:
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
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
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
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:
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
'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 galaxy
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
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