Hi all (and in particular, Scott),
I've just updated my development server and found the following
error when running jobs on our SGE cluster via DRMMA:
galaxy.jobs.runners.drmaa ERROR 2012-09-18 09:43:20,698 Job wrapper
finish method failed
Traceback (most recent call last):
File
Hi Jim,
thanks very much for catching this and providing the fix (I've been away from
email for a few days, so am just getting caught up). I've committed this in
change set 7705:ba64c2178fbe.
Greg Von Kuster
On Sep 17, 2012, at 5:13 PM, Jim Johnson wrote:
Greg,
I think
I'll check it out. Thanks.
- Original Message -
Hi all (and in particular, Scott),
I've just updated my development server and found the following
error when running jobs on our SGE cluster via DRMMA:
galaxy.jobs.runners.drmaa ERROR 2012-09-18 09:43:20,698 Job wrapper
finish
I have to admit that I'm a little confused as to why you would
be getting this error at all - the job variable is introduced
at line 298 in the same file, and it's used as the last variable
to check_tool_output in the changeset you pointed to.
(Also, thanks for pointing to it - that made
Is it possible that you are looking at different classes? TaskWrapper's
finish method does not use the job variable in my recently merged code
either (line ~1045), while JobWrapper's does around line 315.
cheers,
jorrit
On 09/18/2012 03:55 PM, Scott McManus wrote:
I have to admit that I'm
Thanks, Jorrit! That was a good catch. Yes, it's a problem with the TaskWrapper.
I'll see what I can do about it.
-Scott
- Original Message -
Is it possible that you are looking at different classes?
TaskWrapper's
finish method does not use the job variable in my recently merged
On Tue, Sep 18, 2012 at 3:09 PM, Jorrit Boekel
jorrit.boe...@scilifelab.se wrote:
Is it possible that you are looking at different classes? TaskWrapper's
finish method does not use the job variable in my recently merged code
either (line ~1045), while JobWrapper's does around line 315.
Hi again,
I have looked into this matter a little bit more, and it looks like this
is happening:
- tasked job is split
- tasks commands are sent to workers (I am running 8-core high cpu extra
large workers on EC2)
- per task, worker runs env.sh for the respective tool
- per task, worker
The server simply wouldn't start, but log files weren't generated either. This
could be a permissions issue but the folder is g+rw for galaxy, and if I use a
modified run.sh that appends /var/spool/galaxy it works fine.
I'll retry today, could be a heisenbug (or lack of coffee the first time
Interesting. If I'm reading this correctly the problem is happening
inside pkg_resources? (galaxy.eggs unzips eggs, but I think it does so
on install [fetch_eggs] time not run time which would avoid this). If
so this would seem to be a locking bug in pkg_resources. Dannon, we
could put a guard
Hi,
General:
Is there a quantifiable difference in data uploads, speed of processing,
general availability after the connection was/is established to Pittsburgh?
Specific:
If we loaded data to a common directory on an XSEDE resource, would our
students be able to fetch this data in a more
Hi Ken,
You will need to install Cuffmerge and then link it in the same way that
the other tools were added. This wiki has details: a link to the
dependencies (versions) and how to configure paths/ENV set up:
http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies
If you need more help,
Hi Dan,
We are trying to export some sequence to galaxy main from FlyMine but
get the error:
*Error executing tool: Unable to create output dataset: object store is
full*
After switching to galaxy test, it works.
The same error occurred in other mines, could anyone in your team take a
On Sep 15, 2012, at 11:05 PM, Jeremy Goecks jeremy.goe...@emory.edu wrote:
is there a way to determine whether Trackster is the cause?
The only place where Trackster caches data is in the SummaryTreeDataProvider.
In galaxy-central, the relevant line is 709 in
Hello Fengyuan,
Thanks for reporting the problem. We believe that the issue with Object
store has been resolved - would you please try this again and let us
know if there are still problems?
Thanks!
Jen
Galaxy team
On 9/18/12 3:37 AM, Fengyuan Hu wrote:
Hi Dan,
We are trying to export
Hello,
I need to create a job to return a file for it, only need to create a job
beyond what is already created during the execution of my tool because the
data they need to return is the result of a process that runs in the
background.
Can someone help me?
Hugs.
--
*Alfredo Guilherme*
*
*
Ok - that change was made. The difference is that the change
is applied to the task instead of the job. It's in changeset
7713:bfd10aa67c78, and it ran successfully in my environments
on local, pbs, and drmaa runners. Let me know if there are
any problems.
Thanks again for your patience.
Sorry - that's changeset 7714:3f12146d6d81
-Scott
- Original Message -
Ok - that change was made. The difference is that the change
is applied to the task instead of the job. It's in changeset
7713:bfd10aa67c78, and it ran successfully in my environments
on local, pbs, and drmaa
Hello Lance,
I've just committed a fix for getting updates to installed tool shed
repositories in change set 7713:23107188eab8, which is currently available only
in the Galaxy central repository. However, my fix will probably not correct
the issue you're describing, and I'm still not able to
Hello Kevin,
On Sep 14, 2012, at 3:48 AM, kevyin wrote:
Hi,
I have a tool on the main galaxy toolshed called fastq_groomer_parallel.
During an update, with a new tar.gz upload I accidentally included in an
unrelated big folder of stuff under the folder build/
The upload failed (with no
I'd like to have a tool that does not actually return anything (is
that possible?) but writes a file to the directory where Galaxy stores
uploaded data files, and tells Galaxy about it (perhaps that involves
writing to a database?). My tool is written in R.
Here is my scenario:
I want the user to
The filter on the tophat2 fusions output wasn't being evaluated correctly when
settingsType is preSet since the param dict wouldn't then have an entry for
'fusion_search'
$ hg diff tools/ngs_rna/tophat2_wrapper.xml
diff -r 3f12146d6d81 tools/ngs_rna/tophat2_wrapper.xml
---
The bug manifests itself when running the tool with use Defaults selected
results in the following error:
cp: cannot stat
`/data/galaxy-dev/galaxy-dev/database/job_working_directory/000/281/tophat_out/fusions.out':
No such file or directory
It seems that somehow, the filter on the
Fixed in -central changeset 05a172868303
Thanks,
J.
On Sep 18, 2012, at 4:57 PM, Jim Johnson wrote:
The filter on the tophat2 fusions output wasn't being evaluated correctly
when settingsType is preSet since the param dict wouldn't then have an entry
for 'fusion_search'
$ hg diff
Dan, I may not be following, but why not make the serialized R object
a dataset (of its own datatype). Then the user can just pass it to the
downstream tools just by specifying one parameter.
-- jt
On Tue, Sep 18, 2012 at 3:00 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
I want the user to
Hi James,
I realize I didn't do a good job explaining, but your suggestion
sounds promising. How can I make something into a dataset?
Here's what I'm hoping to achieve:
User runs Tool1, uploading a text file and specifying some parameters.
Tool1 uses this to write out a serialized R object.
Thanks for the quick fix!
On 18/09/12 17:56, Jennifer Jackson wrote:
Hello Fengyuan,
Thanks for reporting the problem. We believe that the issue with
Object store has been resolved - would you please try this again and
let us know if there are still problems?
Thanks!
Jen
Galaxy team
On
Hi Greg,
Thanks for the toolshed links I'll make sure to go over them.
I think when the upload failed, mercurial didn't get to the point of
tracking the build folder.
From a mercurial point of view there seems to be no issue, pulling/cloning
or even installing is fine because it's not tracked.
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