1 0 * * 0 0
A 1 RG:Z:rg2
[haruhotz@xenon1 20130912]$
Alternatively, if everything fails, and all you wanna do is just
removing the seven lines at the top of the sam file, you can also use
the tool: Text Manipulation - Remove
Hi Adam
I guess the latest is written down in the notes for the GalaxyAdmins BoF
at GCC2013, see:
http://wiki.galaxyproject.org/Events/GCC2013/BoF/GalaxyAdmins
maybe we can discuss this again at the next 'meetup'?
The next 'meetup' is scheduled for September 18, but I don't know
whether
Hello all,
Another day, another bug report :(
Yesterday I updated this repository, including the README file
which now uses reStructuredText markup:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/fd0c284a245c
After that change, I couldn't view this repository on the Test Tool Shed:
Dear Jeremy
Thank you for your reply and sorry for not being clear. In short I
solved the problem. Below is some info, in case this is useful for
someone else.
Thanks for your help
The situation was:
On Main:
Visualisation of the SAM/BAM file - OK
Visualisation of the VCF file - OK
On my
Hi Pieter,
yes that is possible. Have a look at other repositories. You can only
choose between different tool versions, it there are more than one
'installable version' of a tool. It is not the case in your example.
Lets imagine I only fix some help text in the tool. I do not want to
have
Ok, cool...I get the picture.
One small downside is that then admin has to trust the developer has the
discipline and sound judgment to correctly increase version numbers when
applicableI'm just thinking of scenarios where there is a bad update
released and the admin would like to quickly
Hello Pieter,
Bjoern is correct here for tools, and the same behavior occurs for other Galaxy
utilities that may be contained in tool shed repositories ( e.g., tool
dependency definitions, repository dependency definitions, custom datatypes,
etc ). Each type of Galaxy utility is associated
This scenario should be hopefully handled by the automated nightly tests that
run on repositories in the test and main Galaxy tool sheds. This test
framework does not yet provide full coverage, but it eventually will. Each
repository that has been tested includes a Tool test results container
Hi Dan,
Thanks for the solution! It did help me to identify a missing index
file. I think the indexing run of that particular config maf file
failed for some reason. Since I don't expect much interesting thing on
that, I just remove that for now.
==
Hi Pieter,
to manipulate the ordering of tools is currently not trivial, as far as
I know. You can add label into your shed_tool_conf.xml and tool_conf.xml
file and they should appear and stay. The final ordering will be a merge
of all your *_tool_conf.xml files into the
It looks like there was never a response, but I was looking at a
distantly related issue and came across this thread. If you eliminate
the email hidden parameter and just use:
dynamic_options=getExperiments(__trans__.user.email)
Would that work for your use case?
-John
On Tue, Sep 25, 2012 at
Hi all,
I was wondering if the web interface for the Tool Shed could
allow us to look back at old test results?
This would be useful in connection with explicit revisions to
the tool concerned, but also when something changed which
was external to the tool (e.g. a change in Galaxy itself, or
the
Peter,
I've managed to duplicate that issue on my local tool shed instance, and
hope to have a fix submitted soon.
--Dave B.
On 09/12/2013 05:51 AM, Peter Cock wrote:
Hello all,
Another day, another bug report :(
Yesterday I updated this repository, including the README file
which now
On Thu, Sep 12, 2013 at 2:40 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
I've managed to duplicate that issue on my local tool shed instance, and
hope to have a fix submitted soon.
--Dave B.
Thanks Dave,
Note it seems to be OK at the moment within the RST of a tools
help text, e.g.
This isn't an easy question to answer. Here's why:
*there is significant variation in mammalian genome size; of course, larger
genomes require more resources, but the relationship is difficult to quantify;
*assembly can take anywhere from a day to a week depending on software and
resource
Another vote for the excellent modules system from us at AgResearch. I think
it's the only sane way to manage PATH, etc, when you have multiple versions
of tools installed.
http://modules.sourceforge.net/
I know I've said this before here. Tell all your friends. ;-)
Galaxy's dependency
On Thu, Sep 12, 2013 at 2:01 PM, Mathieu Bahin mathieu.ba...@irisa.fr wrote:
Hi all,
We have been developing our own Galaxy instance for a while now. We have a
cluster on which the job are sent to be executed, it is managed through SGE.
Usually, communication between SGE and DRMAA is ok and
Setting the environment for each tool just prior to running the tool is
clearly better.
What I'm doing currently is loading an environment module just before running
a tool in Galaxy.
On our HPC cluster, I have configured Galaxy to source the following
from our modules system:
1) Global
Hi all,
We have been developing our own Galaxy instance for a while now. We have a
cluster on which the job are sent to be executed, it is managed through SGE.
Usually, communication between SGE and DRMAA is ok and we don't have any
problem with that.
When a job is deleted by the user, most
On Thu, Sep 12, 2013 at 4:22 PM, Dave Bouvier d...@bx.psu.edu wrote:
Thanks for the additional information, Dan has committed a fix in
10592:ea0c57f1cdf0, which is now running on the test tool shed.
--Dave B.
Thanks - in the short term I will try to avoid accents in my README.rst
files
Hi Bjoern,
Thanks, that is helpful information. Updates to new revisions seem to work
fine, i.e. the order as configured in shed_tool_conf.xml seems to be preserved.
We are now facing what I think could be a small bug in the $PATH_TO_IMAGES part
as documented in
Thanks for the additional information, Dan has committed a fix in
10592:ea0c57f1cdf0, which is now running on the test tool shed.
--Dave B.
On 09/12/2013 09:44 AM, Peter Cock wrote:
On Thu, Sep 12, 2013 at 2:40 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
I've managed to duplicate that
Hi Hans-Rudolf, Adam,
As the BoF page indicates, we decided not to do this, for the reasons
listed on the page. So, for now, we won't create a separate email list, or
use MailMan topics (which I had high hopes for).
However, we may not be done with this yet. The plan is still to move
Is there any website or wiki that discusses scaling and hardware requirements
(RAM, processors, hard drives) in more detail, e.g.
- re-sequencing (e.g. align John Doe's sequencing fastq's to the standard human
genome/ make SAM/ make BAM and determine the variants)
- metagenomics (e.g. sequence
Hi guys,
We discovered that the problem is at our apache configuration side...working on
it now... ;)
Regards,
Pieter.
-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Lukasse, Pieter
Sent: donderdag 12 september
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