where are those columns
set on the metadata? Is it stored, generated from the input file? My files are
not official formats, just tsv subclasses.
I’m on changeset 14567:007f6a80629a in galaxy-dist.
cheers,
—
Jorrit Boekel
Proteomics systems developer
BILS / Lehtiö lab
Scilifelab Stockholm
No, I am not subclassing from Tabular. But when I do, it suddenly works. Thanks
loads Dan!
cheers,
—
Jorrit Boekel
Proteomics systems developer
BILS / Lehtiö lab
Scilifelab Stockholm, Sweden
On 07 Nov 2014, at 19:07, Daniel Blankenberg wrote:
> Hi Jorrit,
>
> Are you subclassing
(testing on AWS free tier), but I've tried
m1.large, and that didn't help. I noted that the snapshot ID is always
the same. Since the AMI is from March 2011 (at least the one I select
manually), I assume that I have something wrong in my settings or that
Amazon has changed something
Dear list,
As a first attempt to put my tools in the cloudman/galaxy environment, I
have tried to just crudely copy them to their respective directories,
along with tool_conf.xml. This worked, but some tools raise errors upon
loading them that I cannot reproduce in my local Galaxy instance
(n
Dear list,
I have stumbled on some strange behaviour when uploading files to galaxy
via the upload.py tool. At times, the upload seems to be stalled in
history and is never actually performed, followed by a seemingly
infinite history update (see log below). My system is Ubuntu 11.10 and
runs
ge system
b) ...eventually, unless the user has deleted the history item, it does turn
green and the job is listed as 'ok'.
Do you experience this problem with all files, even small ones?
Regards, Hans
On 02/22/2012 10:14 AM, Jorrit Boekel wrote:
Dear list,
I have stumbled on s
Dear list,
I encountered problems when using galaxy with ubuntu's epiphany browser.
It seems that when using this browser, HTTP_ENVIRON's locale setting is
sometimes 'en-us', but sometimes ' en-us'. That's a whitespace before
the locale. I solved the problem by adding a simple .strip() in
egg
. If there was
a "tar all sets in library and import to history" I'd be using that, but
I've only encountered "tar/zip sets and download locally" which would be
a bit of a workaround.
I haven't found much on this subject in the mailing list, has
Van: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Jorrit Boekel
Verzonden: woensdag 22 februari 2012 10:15
Aan: galaxy-dev@lists.bx.psu.edu
Onderwerp: [galaxy-dev] uploads stuck in history
Dear list,
I have stumbled on some strange behaviour when uploading
e fix (two lines or
so in sge.py).
cheers,
jorrit boekel
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I now see that there is already support for this in the current repo,
but I was using the cm.tar.gz in the default cloudman bucket, which is
older and doesn't have the ubuntu 12.04 support.
My mistake, pretend you never saw it.
cheers,
jorrit
On 05/11/2012 12:27 PM, Jorrit Boekel
Hi,
Hanging uploads have been a problem before with small and large files:
http://comments.gmane.org/gmane.science.biology.galaxy.devel/4583
I don't know if it's been fixed, but it seemed to depend on browser
choice and on what server was running. I was recommended to use the
nginx server IIRC
emand for this sort of function,
but if anyone else would like to use/modify it, I can fork and issue a
pull request.
cheers,
jorrit
On 03/06/2012 06:56 PM, Nate Coraor wrote:
On Feb 29, 2012, at 11:34 AM, Jorrit Boekel wrote:
Dear list,
Our lab's proteomics data is frequently outputt
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Jorrit Boekel
Sent: Thursday, 25 October 2012 8:35 PM
To: Peter Cock
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] the multi job splitter
I keep the files matched by keeping a _task_%d suffix to their names.
So each task is
such?)
Cheers,
-Piotr
*From:*Jorrit Boekel [mailto:jorrit.boe...@scilifelab.se]
*Sent:* Wednesday, July 31, 2013 8:18 PM
*To:* Khassapov, Alex (CSIRO IM&T, Clayton)
*Cc:* p.j.a.c...@googlemail.com; jmchil...@gmail.com;
galaxy-dev@lists.bx.psu.edu; Szul, Piotr (ICT Centre, Marsfield);
Burdet
currently set to 2. However, 5 tasks are run
simultaneously, leading to memory problems.
Am I overlooking something that anyone knows of?
cheers,
jorrit boekel
--
Scientific programmer
Mass spec analysis support @ BILS
Janne Lehtiö / Lukas Käll labs
SciLifeLab Stockholm
). I don’t know
where to go from here with debugging, but has anyone seen anything similar?
Right now it feels like it may be caused by timing rather than actual code
problems.
cheers,
—
Jorrit Boekel
Proteomics systems developer
BILS / Lehtiö lab
Scilifelab Stockho
I should probably mention that the data filesystem is NFS, exported by the
master from /mnt/galaxy/data and mounted on the worker. No separate fileserver.
Master is the one that hangs.
cheers,
—
Jorrit Boekel
Proteomics systems developer
BILS / Lehtiö lab
Scilifelab Stockholm, Sweden
On 07
It seems to be an NFS related issue. When I run a separate VM as an NFS server
that hosts the galaxy data (files, job workdir, tmp, ftp), problems are gone.
There’s probably an explanation for that, but I’m going to leave it at this.
cheers,
—
Jorrit Boekel
Proteomics systems developer
BILS
://bitbucket.org/glormph/adapt/commits/86ec8b1cfeb737dfa31a1b6faf18d918bea7b4c3
I started implementing it in datatypes (first commit), but moved it to tool
config instead. If this is really interesting I guess I can submit a pull
request, but it felt a bit hacky at the time.
cheers,
—
Jorrit Boekel
(as galaxy user, or whoever owns the tools)?
cheers,
—
Jorrit Boekel
Proteomics systems developer
BILS / Lehtiö lab
Scilifelab Stockholm, Sweden
On 31 May 2014, at 01:53, Isabelle Phan wrote:
> Hello,
>
> I'm following "Managed Tool Dependencies" to the letter and sti
the default behaviour when deleting jobs in the UI is
that they keep running but hidden, or is there something wrong in my
config? Is there a way to change this with a setting?
cheers,
jorrit boekel
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ole thing feels a bit like a hack, so I wanted to ask if there is
a way for tools to generate composite files the same way uploads can.
cheers,
jorrit boekel
___
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in you
Dear list,
I am running galaxy-dist on Amazon EC2 through Cloudman, and am using
the enable_tasked_jobs to run jobs in parallel. Yes, I know it's not
recommended in production. My jobs usually get split in 72 parts, and
sometimes (but not always, maybe in 30-50% of cases), errors are
returned
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
solve this in
a non-hackish way, so until someone finds out, I may use reading from a
'eggs_extracted.txt' file to determine if the eggs have been extracted.
And locking the file when writing to it of course.
cheers,
jorrit
On 09/14/2012 10:57 AM, Jorrit Boekel wrote:
Dear list,
24 PM, James Taylor wrote:
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.
becomes a zombie or something, but since it's a
small script, this may do the job. If anyone sees more problems, I'd be
happy to know.
cheers,
jorrit
On 09/19/2012 09:16 AM, Jorrit Boekel wrote:
For completeness, here's two tracebacks (there were more similar ones)
from the sam
Odd, it works for me on EC2/Cloudman.
jorrit
On 09/19/2012 03:29 PM, Peter Cock wrote:
On Tue, Sep 18, 2012 at 7:11 PM, Scott McManus wrote:
Sorry - that's changeset 7714:3f12146d6d81
-Scott
Hi Scott,
The good news is this error does seem to be fixed as of that commit:
TypeError: check_to
Dear list,
I thought I was working with fairly large datasets, but they have
recently started to include ~2Gb files in sets of >50. I have ran these
sort of things before as merged data by using tar to roll them up in one
set, but when dealing with >100Gb tarfiles, Galaxy on EC2 seems to get
Hello-,
I have had similar problems, and you can possibly solve them by using
composite datasets, which allow you to pass files to a directory whilst
having a primary file that represents the dataset (I believe Rgenetics
uses a primary HTML file containing hyperlinks to the files in the dir).
eventually get around to it.
-John
John Chilton
Senior Software Developer
University of Minnesota Supercomputing Institute
Office: 612-625-0917
Cell: 612-226-9223
Bitbucket: https://bitbucket.org/jmchilton
Github: https://github.com/jmchilton
Web: http://jmchilton.net
On Mon, Oc
Dear list,
Our analysis pipeline is normally fed with proprietary raw file types
from mass spectrometry instruments. These can currently only be read on
windows systems where vendor DLLs are installed.
Since Cloudman/Galaxy does not interface with Windows nodes out of the
box, I implemented
Dear list,
In my galaxy fork, I extensively use the job splitters. Sometimes
though, I have to split to different file types for the same job. That
raises an exception in the lib/galaxy/jobs/splitters/multi.py module.
I have turned this behaviour off for my own work, but am now wondering
whe
On 10/25/2012 10:54 AM, Peter Cock wrote:
On Thu, Oct 25, 2012 at 9:36 AM, Jorrit Boekel
wrote:
Dear list,
In my galaxy fork, I extensively use the job splitters. Sometimes though, I
have to split to different file types for the same job. That raises an
exception in the lib/galaxy/jobs
On 10/25/2012 11:25 AM, Peter Cock wrote:
On Thu, Oct 25, 2012 at 10:00 AM, Jorrit Boekel
wrote:
On 10/25/2012 10:54 AM, Peter Cock wrote:
On Thu, Oct 25, 2012 at 9:36 AM, Jorrit Boekel
wrote:
Dear list,
In my galaxy fork, I extensively use the job splitters. Sometimes though,
I
have to
On 10/25/2012 12:02 PM, Peter Cock wrote:
On Thu, Oct 25, 2012 at 10:35 AM, Jorrit Boekel
wrote:
My question is still though if it would be bad to not raise an exception
when different filetypes are split in the same job.
In general splitting multiple files of different types seems dangerous
etwork problems, etc?
If not, would it be hard to implement?
cheers,
jorrit boekel
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This may be implemented, I believe some people run Galaxy on the cluster,
but if not:
Galaxy normally operates on files stored in the database/files folder. If
your Galaxy instance has access to the files you need on your parallel fs,
I guess you could start by writing a tool that creates links to
If one could upvote pull request, I'd be doing that now!
thanks loads John,
jorrit
On 12/05/2012 07:14 PM, John Chilton wrote:
Here is my video-based sales pitch for multiple file datasets
(specifically pull request 86 and 87 and subsequent future pull
requests).
http://www.youtube.com/watch?v
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