Alex,
Thanks for the assistance!
The modules work fine, since i see them in the log files. The id and gid match
the output of id galaxy. I think the problem lies somewhere else.
Kind regards
Joachim
"Bossers, Alex" schreef:
>Joachim,
>If I remember correctly for our galaxy proftpd setup o
Hi Rob,
The 'bed' datatype in Galaxy refers to UCSC's Browser Extensible Data format
(http://genome.ucsc.edu/FAQ/FAQformat.html#format1).
Is this a binary PLINK .bed file
(http://pngu.mgh.harvard.edu/~purcell/plink/binary.shtml)? If so, you may want
to consider looking at/using the 'pbed' data
On Jul 13, 2012, at 2:52 PM, Iry Witham wrote:
> Will the runner0.log or web0.log be sufficient? If not what would you
> like?
If you have updated to a relatively recent version of Galaxy, be sure that you
updated to the web/manager/handler configuration from the web/runner
configuration:
On Jul 13, 2012, at 1:22 PM, Nate Coraor wrote:
> On Jul 9, 2012, at 5:53 AM, Peter Cock wrote:
>
>> Hi,
>>
>> I'd also be interested in the current cross-browser support.
>> We're recommending people use Firefox or Chrome here
>> for our local Galaxy.
>>
>> We've noticed problems under Intern
Will the runner0.log or web0.log be sufficient? If not what would you
like?
Iry
On 7/13/12 2:23 PM, "Nate Coraor" wrote:
>On Jul 13, 2012, at 9:05 AM, Iry Witham wrote:
>
>> Hi Nate,
>>
>> I have set this as shown below:
>>
>>
>> # The URL for the default runner to use when a tool does
On Jul 13, 2012, at 9:05 AM, Iry Witham wrote:
> Hi Nate,
>
> I have set this as shown below:
>
>
> # The URL for the default runner to use when a tool doesn't explicitly
> define a
> # runner below.
> default_cluster_job_runner = pbs:-l nodes=1:ppn=1,walltime=20:00:00
This should be
On Jul 9, 2012, at 4:55 PM, Moore, Raymond M. wrote:
> Thank you Peter,
>
> That's exactly what I was looking for. I'd really like to implement
> the functionality defined by John Chilton.
>
> The ability to select a queue based on the input size is very important
> to our group.
>
> Thanks a
On Jun 27, 2012, at 5:59 PM, Dorset, Daniel C wrote:
> We have an instance of Galaxy deployed on a local institutional cluster. It’s
> working well, but when we import BED files for visualization, Galaxy runs the
> processing for these on the cluster. I would like to run these tasks locally
> i
To:
From: James Taylor
Subject: Re: [galaxy-dev] List of browsers which supports galaxy
Quoting Nate Coraor (2012-07-13 17:22:22)
> We don't maintain an official list except with Internet Explorer, for which
> support was dropped recently, as Peter noted above.
We do attempt to continue to sup
Hi, Peter.
A couple of things worth checking:
1) Is the file (it's a perl script) executable by the user running the
Galaxy process? Unfortunately the FastQC distro is built in windows
apparently so that script is not executable out of the box - fixing
that may be all you need to do.
2) Does fas
Hi Nate,
I don't think that it does. We get the bed files from our GWAS pipelines.
We were able to upload the file by adding 'bed' to the list of
unsniffable_binary_formats in binary.py and manually specifying the format.
Do you think this could cause problems later?
-Rob
On Thu, Jul 12, 2012 at
I get the following error when attempting to run FastQC from galaxy:
job command line:
python /opt/galaxy/galaxy-dist/tools/rgenetics/rgFastQC.py -i
/opt/galaxy/galaxy-dist/database/files/000/dataset_75.dat -d
/opt/galaxy/galaxy-dist/database/job_working_directory/000/114/dataset_128_files -o
On Jul 9, 2012, at 11:25 AM, Sascha Kastens wrote:
> Hi!
>
> Unfortunately I was not able to fix this problem yet.
>
> Is anybody out there who had a similar problem while using Galaxy with SGE or
> has the knowledge about the things I can look at?
Hi Sascha,
The error message you are getti
On Jul 9, 2012, at 5:53 AM, Peter Cock wrote:
> Hi,
>
> I'd also be interested in the current cross-browser support.
> We're recommending people use Firefox or Chrome here
> for our local Galaxy.
>
> We've noticed problems under Internet Explorer, e.g. the 'peek'
> effect for clicking on history
Joachim,
If I remember correctly for our galaxy proftpd setup on ubuntu 10.10.
Be sure to compile proftpd with the required additional SQL modules.
Then figure out the user and group ids of galaxy user that can access the DB
(mysql in our case).
$ id galaxy (or whatever user you use)
Make sure
Hi Robert,
It's probably fine, although you lose the benefit of datatype sniffing. The
binary detection is there to prevent abuse on our public site. This error
should really only occur if there's a non-ASCII character in your bed file, so
you may want to check it programatically, e.g. (slowl
Hello Luobin,
Your information really helped narrow down the problem, and I've committed what
I believe is a fix in change set 7388:28b3364341b6, which is currently
available in the Galaxy central repository. This fix should be available in
the next Galaxy dist update, which should be availabl
Dear Galaxy devs,
I am setting up an ftp server with authentication to the Galaxy user
tables, but the password is not recognized as being correct.
joachim@joachim-laptop:~$ ftp 192.168.10.23
Connected to 192.168.10.23.
220 Welcome to BITS Galaxy FTP server.
Name (192.168.10.23:joachim): joach
Hi Nate,
I have set this as shown below:
# The URL for the default runner to use when a tool doesn't explicitly
define a
# runner below.
default_cluster_job_runner = pbs:-l nodes=1:ppn=1,walltime=20:00:00
Iry
On 7/12/12 4:29 PM, "Nate Coraor" wrote:
>On Jul 6, 2012, at 12:32 PM,
Hi Geoff,
I encountered the same issue configuring proftpd - thanks for mentioning
this issue.
Would you mind sharing how you exactly solved the issue with the uid/gid
of the galaxy user? I want not to change the uid/gid of this user as it
is the same on other machines here.
Joachim
Thanks. I was first looking at the wrong base_panels.mako: but restoring
the file in /templates/base_panel.mako fixed the problem.
Regards,
Joachim
Joachim Jacob, PhD
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@
Hi Nate,
I kept keeping the errors untill I restarted galaxy completely. I could
still submit jobs to the HPC queue from other programs. I'm not very
familiar with python, but if you have pointers on where to start to
solve this, I might be able to contribute. If it would be possible to
resta
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