At Thu, 10 Oct 2013 00:31:56 -0500,
John Chilton wrote:
>
> Simon, using your test tools I was able to reproduce your errors. Pull
> request 233 is my attempt to fix them with a lighter touch than just
> immediately converting outputs to ascii. Do these patches work on your
> end?
>
> Bjoern, do
At Fri, 4 Oct 2013 23:12:01 -0500,
John Chilton wrote:
> I understand the desire to not want to try to execute the tool shed
> actions if tool_shed_packages are not specified in the dependency
> resolvers list. I have created a Trello card for it
> (https://trello.com/c/CPeU3VlR). It sounds like
Dear all,
some SGE instances will add automatically an semicolon add the end of
each command, resulting in a disrupted job, because ';;' are not
allowed.
The latest changes to the Bowtie2 wrapper resulting in such a case and a
crash in our instance. An easy solution would be to fix the wrapper a
Hi Ian,
what mean broken pipe error, can you post the error message here?
Thanks,
Bjoern
> Hello,
>
> I've got a local install of galaxy with fastx tools installed. I'm getting a
> broken pipe error but I'm not sure why. I install fastx using the compiler
> outside galaxy and it was working f
Hello Peter,
I've created teh following Trello card for this:
https://trello.com/c/Vg12cS7o/1174-toolshed-frames-issue-with-readme-file-links
Thanks,
Greg Von Kuster
On Oct 8, 2013, at 10:44 AM, Peter Cock wrote:
> Consider the following sequence:
>
> 1. Goto http://toolshed.g2.bx.psu.edu/
Hi all,
The recent changes to the DRMAA runner are for better handling of job-ending
conditions under slurm, but it looks like SGE has different behavior when a job
finishes. I'll provide a fix for this shortly, in the meantime, it's fine to
use a slightly older version of drmaa.py.
--nate
O
Hi Olivia,
Our development team suggests checking the paster.log, plus, if
applicable, proxy server logs.
From what we know, this kind of issue generally indicate a firewall
issue, but without more information, it is difficult to diagnose.
Please keep replies on this mailing list instead (i
Hello,
I've got a local install of galaxy with fastx tools installed. I'm getting a
broken pipe error but I'm not sure why. I install fastx using the compiler
outside galaxy and it was working fine inside galaxy previously. Fastx works
fine via the command line. I've checked the xml files and I
On Oct 9, 2013, at 5:40 PM, Gonsky, Rivkah, Ph.D wrote:
> Link doesn’t work
Hi Rivkah,
If you're referring to the Galaxy instance at usegalaxy.org, this has been
fixed.
Thanks,
--nate
>
> Rivkah Gonsky
> Inflammatory Bowel and Immunobiology Research Institute
> Davis 4063
> 8700 Beverly Blv
Hi,
Our Galaxy instance is configured to use LSF. The problem is that
sometimes our jobs get preempted (stopped and re-queued to let
higher-priority jobs run) and Galaxy thinks that those jobs have failed.
Is there any way around that by any chance?
Thanks,
Ilya
___
Hi James,
The FASTX fastq to fasta conversion tool requires your input to be in one of
the "fastqsanger,fastqsolexa,fastqillumina" datatypes. Please note that this
does not include the base "fastq" datatype. Can you double check the datatype
assigned to your datasets?
Alternatively, there is a
On Tue, Oct 8, 2013 at 5:03 PM, Adhemar wrote:
> Hi,
> After the last update I'm getting the following error.
> The job is submitted to SGE e executed, but galaxy doesn't get the result
> and keeps showing the job is executing (yellow box).
> Any clues?
> Thanks,
> Adhemar
>
>
>
> galaxy.jobs.runn
Thank you Jeremy,
It turned out the issue was our version of bedtools. We updated to 2.17.0
and no longer have the errors.
Cheers,
Liisa
From: Jeremy Goecks
To: Liisa Koski
Cc: "galaxy-dev@lists.bx.psu.edu Galaxy-dev"
Date: 05/10/2013 08:08 PM
Subject:Re: [galaxy-dev
Hi all,
I really can't understand why this should be, but in recent versions of Galaxy
if you have a simple html page with an iframe embedding Galaxy, you loose the
masthead (no login, workflow etc) and the history panel no longer works.
eg (newer Galaxy Versions)
https://galaxy.cbio.mskcc.org
So I have used Galaxy to convert >50 different FASTQ files into FASTA with no
problems before over the past year. The sequencer and FASTQ file format have
been identical, however, yesterday when I tired to use the the FASTQ to FASTA
converter I couldn't get it to recognise my files.
The drop d
On Wed, Oct 9, 2013 at 10:01 PM, Björn Grüning
wrote:
> Am Mittwoch, den 09.10.2013, 19:15 +0100 schrieb Peter Cock:
>> On Tue, Oct 8, 2013 at 9:57 PM, Dave Bouvier wrote:
>> > Peter, Björn,
>> >
>> > I have restored gfortran to the repository test host. I believe it was
>> > inadvertently remove
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