Hello gurus,
I made some slight progress...
If I specify a handlers section into the job_conf.xml file with:
Then galaxy would at least start. However, it is not very functional, I
can't upload files or run job, it says:
An error occurred with this dataset:*Unable to run j
Hi, Richard,
I see you are looking in the main toolshed. I cant speak for fcarmia's one
but it doesn't do any dependency installation. The 'digital_dge' one was
deprecated - I've now deleted it.
The differential count models package in the statistics section of the test
toolshed -
http://testtools
On Tue, Apr 30, 2013 at 9:46 AM, Scott Hazelhurst
wrote:
> Below that is the output I get in the log. From the torque log it complains
> that there is no default queue specified.
Hi Scott,
Today I was hit by what it seems the same issue. In my case it was an
issue with my torque server. I failed
Dear Nate,
Actually... no, galaxy's home was set to a non-existent directory so
the working directory was being changed to the root of the file system.
However the script still seemed to work. I changed the script to use "su -
galaxy -c" like you show anyway. There seem to be no significant ch
Hi,I was very excited to see the re-run option and associate with paused jobs option working very well..I was hoping to be able to re-run a job like this from the API, but cannot seem to find any API calls that corresponds to this here:http://galaxy-dist.readthedocs.org/en/latest/lib/galaxy.webapps
I don't think it's a memory issue (but what made you say that?) since each process is hardly using any memory, although VIRT memory in top is showing 2.7GB per python process, RES is only ever going to 250MB and I have a 16GB machine (although SWAP is only 4GB but not using any of the swap either,
On Aug 9, 2013, at 11:53 AM, Seth Sims wrote:
> Dear Nate,
>
> Adding "su - galaxy" as the first line of the pre-start script seems to
> work reasonably well. Also it looks like the line that sets the egg cache is
> not working properly. My egg cache ends up being "/tmp/${SERVER_NAME}_egg/"
On Aug 2, 2013, at 1:06 PM, Thon de Boer wrote:
> I did some more investigation of this issue
>
> I do notice that my 4 core, 8 slot VM machine has a load of 32, with only my
> 4 handler processes running (Plus my web server), but not even getting more
> than 10% of the CPU each.
> There seems
Hello,
I have some questions about the edgeR (fcaramia) and digital_dge (fubar)
repositories in tool shed.
What is the difference between the two respositories in terms of being able
to run edgeR?
What is the proper way to install R so that the tool wrappers can use edgeR?
What versions of R and
Original Message
Subject: Re: how to add settings of TMPDIR=/scratch for sge/drmaa in
universe_wsgi.ini
Date: Tue, 13 Aug 2013 23:21:16 -0700
From: tin h
To: Jennifer Jackson
CC: Galaxy Dev
Thank you Jennifer.
I am not sure if my previous email got gabled u
Hi
just to keep things up to date I have the the cluster up and running jobs
are being submitted. Last problem I am facing is:
21: UCSC Main on Pig: refGene (chr18:1-61220071)
error
An error occurred with this dataset: *The remote data source application
may be off line, please try again later.
Also through toolshed, version 0.5.9-r16. An example error on our part is
(SamToBam):
Error extracting alignments from
(/galaxy/galaxy-dist/database/files/067/dataset_67090.dat), [samopen] SAM
header is present: 25 sequences.
Parse error at line 261924: sequence and quality are inconsistent
Abo
Björn,
Thank you for the report, I've created a trello card to track the
progress of this issue:
https://trello.com/c/ZXgnlXfo/1049-toolshed-repository-export-fails-when-a-repository-s-long-description-contains-special-characters
--Dave B.
On 8/14/13 04:54:06.000, Bjoern Gruening wrote:
There aren't any database-specific tests, but if you could get more details
from your sysadmin regarding the issues they're seeing, I'd be very
interested in seeing it.
You could run the usual functional tests to verify galaxy itself is
functional: http://wiki.galaxyproject.org/Admin/Running%20Tes
Hi,
I've been getting some errors on our local Galaxy instance which haven't
been solved by updating to the latest code.
Some of them involve sql-type errors. My sys-admin informed me that "There
are a couple of SQL errors being reported, i.e. text attempting to be
inserted into an integer field wi
Peter,
I've created a Trello card for tracking the status of this issue.
https://trello.com/c/32l2NZRn/1048-toolshed-investigate-possibility-of-recording-tool-dependencies-that-time-out-in-the-automated-testing-process
--Dave B.
On 8/14/13 09:40:03.000, Peter Cock wrote:
On Wed, Aug 14, 20
Peter,
Remnants from previously failed installation attempts seems the most
likely explanation, but I'll try to duplicate that situation locally and
see if there's any underlying issue.
--Dave B.
On 8/14/13 09:51:24.000, Peter Cock wrote:
Hi Greg,
I'm seeing something strange on a syste
Hi Greg,
I'm seeing something strange on a system running the August stable
release of galaxy-dist,
$ sudo -u galaxy hg head
changeset: 10393:d05bf67aefa6
branch: stable
tag: tip
user:Nate Coraor
date:Mon Aug 12 11:55:41 2013 -0400
summary: Added tag release_20
On Wed, Aug 14, 2013 at 2:32 PM, Dave Bouvier wrote:
> Peter,
>
> The problem with testing the installation of package tool dependencies,
> especially but not limited to BLAST+, is that the time it takes to compile
> them exceeds the timeout for the automated testing framework, and so it
> termina
Peter,
The problem with testing the installation of package tool dependencies,
especially but not limited to BLAST+, is that the time it takes to
compile them exceeds the timeout for the automated testing framework,
and so it terminates that build step. I am currently working on
enhancing the
On Wed, Aug 14, 2013 at 11:56 AM, Peter Cock wrote:
> Hi Greg,
>
> I'm hoping you (or Dave) can throw a little light on why the
> NCBI BLAST+ nightly tests are not working again yet:
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/949fa0294c0d
>
> e.g. Fatal error: Exit code 127
Hi,
On my local galaxy installation (updated to the latest version yesterday), it takes ages (hours!) to upload a fastq files. I attach a report from the the computer on which galaxy is installed. The fastq file is uploaded from
132.72.88.186. Initially there is an error message (the attached
Through toolshed.
On 14 August 2013 12:50, Bjoern Gruening wrote:
> Hi Moritz,
>
> do you installed bwa through the toolshed or manually?
>
> Cheers,
> Bjoern
>
> > Hey Folks,
> >
> >
> > Is there really nobody that can help Geert and me? Thats quite
> > important to me right now.
> > This is o
Hi Greg,
I'm hoping you (or Dave) can throw a little light on why the
NCBI BLAST+ nightly tests are not working again yet:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/949fa0294c0d
e.g. Fatal error: Exit code 127 () /bin/sh: 1: blastn: not found
/bin/sh: 1: blastn: not found
A
Hi Moritz,
do you installed bwa through the toolshed or manually?
Cheers,
Bjoern
> Hey Folks,
>
>
> Is there really nobody that can help Geert and me? Thats quite
> important to me right now.
> This is obviously not something specific to me, as Geert has the exact
> same error.
> I meanwhile t
Hi Peter,
no nothing BLAST+ related. Greg highjacked that thread to inform me
about the new export functionality.
I will stop posting here.
Cheers,
Bjoern
> Hi Bjoern,
>
> Was this reply on the wrong thread - or is there
> something here related to the BLAST+ binaries?
>
> Thanks,
>
> Peter
>
Hey Folks,
Is there really nobody that can help Geert and me? Thats quite important to
me right now.
This is obviously not something specific to me, as Geert has the exact same
error.
I meanwhile tried to replace the id with "1" but it still doesnt work.
Best
Moritz
_
Hi Bjoern,
Was this reply on the wrong thread - or is there
something here related to the BLAST+ binaries?
Thanks,
Peter
On Wed, Aug 14, 2013 at 10:29 AM, Bjoern Gruening
wrote:
> Hi Greg,
>
> I tried the manifest file and saw that the ordering is not correct. You
> can see that on the last to
Hi Jun,
please have a look at
https://github.com/bgruening/galaxytools/blob/master/chemicaltoolbox/simsearch/simsearch.xml
the else clause will create some symlinks you can use directly with
msconvert. For debugging purpose just add msconvert at first to your
PATH and avoid the $__root_dir__/ h
Hi Bjoern,
Many thanks for your reply.
Here is the wrapper:
Convert non PSI standard mass spectral file into the PSI
standard format mzML
$__root_dir__/../gio_applications/proteowizard/proteowizard.pl
$input $type.input_type $output $output.id $__new_file_path__
Hi Greg,
I tried the manifest file and saw that the ordering is not correct. You
can see that on the last to repositories. Since, chemicaltoolbox is the
meta_repository it should be always the last one.
Cheers,
Bjoern
> Hello Bjoern,
>
>
> I have the export repository ( and optionally all repo
On Thu, Aug 8, 2013 at 2:38 AM, John Chilton wrote:
> On Wed, Aug 7, 2013 at 3:33 PM, Ganote, Carrie L wrote:
>> Hi John,
>>
>> That was it. I feel silly. I still have a lot of tooth-cutting to do on
>> python!
>>
>> I saw the parallel tags in the Blast tool and was very intrigued,
>> but couldn
Hi Greg,
I tried to export the chemicaltoolbox but I only got one tarball called:
capsule_with_dependencies_testtoolshed.g2.bx.psu.edu_chemicaltoolbox_bgruening_4133dbf7ff4d.tar.gz
with only one dependency and no manifest file.
Cheers,
Bjoern
___
Hi Jun,
>
> I have managed to use something like
>
>
>
>
>
>to display the wanted label for the dataset in the
> history.
>
> However when I applied the same code to other tool wrappers, some
> weird things happened: the wrapper can still be loaded in the web
> page, but when
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