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.
B
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 9/
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. Someh
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 wrote:
> I want the user to upload a text file, th
Hi,Jobs that I start on my in-house Galaxy instance now take up to 3-4 min to go from queued to Running, even though there is nothing much going on on the galaxy server...I have been running this instance since June and use a relatively new version of Galaxy-central (Last update, 22-Aug changeset:
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 t
> 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 t
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
--- a/tools/ngs_rna/toph
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
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 (wit
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 r
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 drma
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.
-Scott
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*
*
*
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 som
On Sep 15, 2012, at 11:05 PM, Jeremy Goecks 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
> lib/galaxy/visualization/genome/data_providers
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
loo
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, p
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 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 arou
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
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 runs
On Tue, Sep 18, 2012 at 3:09 PM, Jorrit Boekel
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.
>
> cheers,
> jorrit
Yes exactly
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
>
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
On Tue, Sep 18, 2012 at 2:55 PM, Scott McManus wrote:
>
> 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
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 inves
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
> fini
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 templates/adm
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 "/mnt/galaxy/
For the record - mixed tabs/spaces as delimiters in .loc files seem to
have been the problem (again) - maybe we should log errors when ragged
tab delimited loc tables are provided?
-- Forwarded message --
From: Sandrine Imbeaud
Date: Tue, Sep 18, 2012 at 5:54 PM
Subject: Re: [gala
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