Re: [galaxy-dev] GalaxyToolShed: 'Contact owner'
by Greg Von Kuster
Hi Marcel,
Requiring users to be logged in in order to contact the owner of a repository significantly hinders spam emails.
On Jan 12, 2012, at 9:04 PM, Marcel Schumann wrote:
> Hi Greg,
>
> sure, that's right.
> But I checked it for my own repository _without_ being logged in ... and for other repositories the option was also not available.
>
> Ah, ok, now I see where the problem is: it seems that you have to be logged in in order to contact the owner of a repository! Ok, is this really intended? ;-)
>
> If yes, then the problem is of course that most users who want to search for new galaxy tools will not be logged in (because they probably have no account) and thus cannot contact the owner ... and will not even know that there exists such an option.
>
>
> Cheers,
> Marcel
>
> On 1/12/12 5:55 PM, Greg Von Kuster wrote:
>> Hello Marcel,
>>
>> This option is available for all repositories. If you are looking at a repository you own, the option is not available because it makes no sense to contact yourself. However, anyone else looking at your repository has the option available to them.
>>
>> Thanks!
>>
>> Greg
>>
>> On Jan 12, 2012, at 11:21 AM, Marcel Schumann wrote:
>>
>>> Dear Greg,
>>>
>>> I just noticed that for some repositories there is a 'contact owner' option, which is a very nice idea, I think ...
>>>
>>> However, for my repositories (CADDSuite) this option is not available. Is there any way I can enable this ?
>>>
>>>
>>> Cheers,
>>> Marcel
>>>
>>>
>>>
>>
>> Greg Von Kuster
>> Galaxy Development Team
>> greg(a)bx.psu.edu
>>
>>
>>
>
>
> --
> Marcel Schumann
>
> University of Tuebingen
> Wilhelm Schickard Institute for Computer Science
> Division for Applied Bioinformatics
> Room C313, Sand 14, D-72076 Tuebingen
>
> phone: +49 (0)7071-29 70437
> fax: +49 (0)7071-29 5152
> email: schumann(a)informatik.uni-tuebingen.de
Greg Von Kuster
Galaxy Development Team
greg(a)bx.psu.edu
10 years, 5 months
Re: [galaxy-dev] Picard MarkDups
by Ann Black
Hi Ryan -
I have done similar things with our tools as well. For now I have edited
the xml file to include the following option in the <command> section that
would get passed into the picard script wrapper:
--maxjheap="8g"
I considered exposing this out in the UI, but have teetered on whether to
expose the complexity out to the end user.
Thanks,
Ann
>
>Message: 8
>Date: Thu, 12 Jan 2012 11:37:23 -0500
>From: Ryan Golhar <ngsbioinformatics(a)gmail.com>
>To: galaxy-dev(a)lists.bx.psu.edu
>Subject: [galaxy-dev] Picard MarkDups
>Message-ID:
> <CAFbjochhOioiw7a8t4p0gVs8ZAYWUx82gv4Bjv1RnUZjxC0G-Q(a)mail.gmail.com>
>Content-Type: text/plain; charset="iso-8859-1"
>
>I'm trying to run Picard MarkDups through Galaxy. Picard is using the
>standard 4g for the java max heap size. I need to increase this. Is it
>possible to offer this as an option to the user? If not, where do I
>change
>this? I see the entry in picard_wrapper.py. Do I change it here or in
>the
>XML file for MarkDups?
>
>Ryan
>
10 years, 5 months
Toolshed tools are not run
by Anthonius deBoer
Hi,
I am trying to install some tools from the main toolshed, and the installation went OK for the tool "tabToHtml (really something that galaxy should do out of the box...Show tab data in actual tables, rather than a dump of text).
But when I try to run the tool, it is just marked as queued only and never actually runs...Anyone know what this could be?
Using the latest galaxy-central on a local installation with an SGE cluster.
Thon
10 years, 5 months
AnnoVar tool?
by Ryan Golhar
I thought I once saw a publication (or presentation maybe) talking about
AnnoVar being available in Galaxy but I don't see it online or in
galaxy-dist, nor in the tool shed. Is it really available?
10 years, 5 months
Job in Edinburgh, Scotland
by Alastair Kerr
Dave Clements kindly suggested that I post this to the list.
My team is looking for someone to help out with the ever increasing need
of data analysis in our centre. We support the diverse bioinformatics
needs of 18 groups (http://www.wcb.ed.ac.uk) and currently there are
many large NGS projects. We use galaxy as a central component for rapid
tool development and to enable users in their own research.
Dave (clements(a)galaxyproject.org) has also kindly offered to provide
impartial advice about Edinburgh for those who may not know of the joys
of living here.
It is a fixed term contract for 30 months (which should allow plenty
time to impress groups leaders for more funding).
-Alastair
--
Alastair Kerr, Ph.D.,
Bioinformatics Core Facility Manager,
Wellcome Trust Centre for Cell Biology,
2.21 Michael Swann Building,
The University of Edinburgh, Edinburgh,
EH9 3JR, UK Tel: +44 131-650-7527
Details:
=-=-=-=-=-=-=-=-=
Wellcome Trust Centre for Cell Biology, University of Edinburgh:
Bioinformatics Support Provider
A position is available in bioinformatics support for the Wellcome Centre for Cell Biology at the University of Edinburgh. The successful candidate will work for the Bioinformatics Core Facility to help provide advice, training, analysis and applications to Centre laboratories (see www.wcb.ed.ac.uk )
A key area for support in the centre is the increase in projects using a range of next-generation sequencing techniques (ChIP-seq, RNA-seq etc) and hence skills pertaining to managing and analysing such data is highly desirable.
Funding for this post is, in part, from the EpiGeneSys Network of Excellence (www.epigenesys.eu ) to the Allshire Lab (http://allshire.biology.ed.ac.uk ). Thus the successful applicant will have access to a variety of training courses, scientific workshops and forums run by EpiGeneSys.
Qualifications:
Candidates should have at least an M.Sc. in computational biology/bioinformatics or equivalent.
An understanding of molecular biological processes would also be useful but not essential.
Essential skills:
Some background in molecular biology and statistics. Experience in the Linux command line and at least one scripting language (Perl, Python or Ruby).
Desirable skills:
R-language including BioConductor, databases (mySQL or postgres), Galaxy
platform administration, Linux administration
Salary Scale: Estimated salary: £30,000 to £34,000 GBP - To be confirmed.
Fixed Term: 30 months.
Please contact Robin Allshire robin.allshire(a)ed.ac.uk or Alastair Kerr alastair.kerr(a)ed.ac.uk
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
10 years, 5 months
User name / public name confusion.
by J. F. J. Laros
Dear developers,
Subject: Minor issue - Confusion about public / user name.
Description:
When creating an account or managing user information, the error ``User name
must contain only lower-case letters, numbers and '-''' may occur if the user
chooses an invalid public name. This error can be confusing when the user tries
to search for a ``User name'' field. Perhaps this error should mention the
field name.
With kind regards,
Jeroen.
--
Jeroen F. J. Laros - J.F.J.Laros(a)lumc.nl
10 years, 5 months
SAM/BAM Hybrid Selection Metrics
by Ryan Golhar
Hi all - I think there is a problem with the Picard HSMetrics wrapper in
Galaxy. The wrapper accepts a BAM files and a BED file. However the BED
file isn't really in a BED format...it requires a SAM header before the BED
lines. This really isn't a BED file format. I'm not quite sure how Galaxy
should deal with this...maybe a file format specific for Picard formatted
BED file.
10 years, 5 months
Status on importing BAM file into Library does not update
by Ryan Golhar
I'm adding Data Libraries to my local galaxy instance. I'm doing this by
importing directories that contain bam and bai files. I see the bam/bai
files get added on the admin page and the Message is "This job is running".
qstat shows the job run and complete. I checked my runner0.log and it
registers the PBS job completed successfully. But the web page never
updates. I tried to refresh the page by navigating away from it then back
to it, but it still reads "This job is running". How do I fix this?
10 years, 5 months
Setup galaxy to run on SGE cluster
by Derrick LIN
Hi guys,
I am trying to configure our test galaxy to run on our SGE cluster
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster.
This is my first time to come across to drmaa, so a bit confused.
I installed teh galaxy on a NFS location where can be accessed
clsuter-wide. I have configured in universe_wsgi.ini:
start_job_runners = drmaa
default_cluster_job_runner = drmaa:///
and export the libdrmaa path:
export DRMAA_LIBRARY_PATH=/opt/sge/lib/lx-amd64/libdrmaa.so.1.0
Sound like that's all. But I am not sure how galaxy can actually bind to my
cluster? Anywhere I need to specify the qmaster URL etc?
Or simply configure galaxy host to be a submission host of the cluster, the
galaxy will fetch all information by itself?
Kind regards,
Derrick
10 years, 5 months
