thanks for reply.
On Wed, Aug 24, 2011 at 3:32 AM, Nate Coraor wrote:
> shashi shekhar wrote:
> > Hi,
> >
> > I have local instance of Galaxy and i am doing some modification in
> > Galaxy .So i need tool id id in local.py file . How i will get this
> > information in runner file (l
I get these two error in the log file. The job finishes correctly and a
metadata file is created but I still get the error. Can anyone provide me with
more detail about what this error means? The second error is incorrect because
the files were deleted.
setting metadata externally failed for H
So I figured out that it is job/runners/__init__.py that does the cleanup. But
now I can't figure out how to pass the galaxy username to my script to change
the permission back. I thought os.getlogin() would give me the right username
but it returns my user name and not the galaxy user. Thought
shashi shekhar wrote:
> Hi,
>
> I have local instance of Galaxy and i am doing some modification in
> Galaxy .So i need tool id id in local.py file . How i will get this
> information in runner file (local.py).
Hi Shashi,
Anywhere you have the job_wrapper object, the Job ID can be accessed
sohk...@notes.cc.sunysb.edu wrote:
> Hi,
> I have the production Galaxy setup and running on Mac OS Leopard 10.6,
> with postgres and apache. However, I am unable to run it as daemon. I
> don't get an error, the browser just hangs there.
> Thanks for any advice.
Hi Sohail,
How are you startin
Camille Stephan wrote:
> Hello,
>
> I just installed postgres in my machine and things seem to work fine except
> for the "Upload files from filesystems paths" option which gives the
> following error:
>
> "Invalid paths:
> /path/to/file.fasta
> "
>
> The path is correct and I tried with differe
When running as the actual user in drama, I made it so the .dat files are not
initially created so that when a tool moves data from the a temp directory to
the out .dat file it will not fail. (i.e. unix does not allow moving a file
owned by one user to a file owned by another user because mv car
Great, thanks!!
From: Daniel Blankenberg [mailto:d...@bx.psu.edu]
Sent: Tuesday, August 23, 2011 1:26 PM
To: Chorny, Ilya
Subject: Re: [galaxy-dev] database/files/_metadata_files
Run a tool (or auto-detect metadata) that creates any BAM or MAF output file.
The file will originally be created in
While snooping around the Galaxy code, I noticed that some tool features are
not supported in workflows, only in histories. Is there a list somewhere that
lists the restrictions?
Specifically, are "multiple" inputs supported?
John Duddy
Sr. Staff Software Engineer
Illumina, Inc.
9885 Towne Cent
Hi Ilya,
Tools should not ordinarily write to this directory, but will often read from
it. These files are generated by Galaxy's Metadata functionality. If you are
setting metadata externally (settings in universe_wsgi.ini) and using a
cluster, then this will occur as part of the tool/job scri
Can someone point me to a tool which writes to this directory? I made some
changes to the code to run as actual user but cannot find a tools that writes
to this directory.
Thanks,
Ilya
Ilya Chorny Ph.D.
Bioinformatics Scientist I
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Work
Louise-Amélie Schmitt wrote:
> Hi,
>
> I would need to make a tool that can get the API dataset id out of
> the input dataset of the tool, how can I do that?
Hi L-A,
Pass in as an argument:
$__app__.security.encode_id( 'file.%s' % $input1.id )
Where 'input1' is the param name of your input
Chorny, Ilya wrote:
> When I run galaxy as the actual user using the code I committed to my fork, I
> run into a problem with dataset_*.dat files that have associated data wherein
> the associated data files are copied from the job_working_directory into the
> files directory. That directory is
Hi Shashi,
For information on Galaxy's visualization tool, "Trackster", see:
http://wiki.g2.bx.psu.edu/Learn/Visualization
If you are interested in adding your own visualization tool for e.g. displaying
Galaxy datasets, please see the previously provided information.
Thanks for using Galaxy,
Is there any good reason why Galaxy can't use a more recent version of
samtools? The only difference I can see is the mpileup command. The algorithm
by which mpileup finds SNPs is a little different. Does anyone know if the
file format has changed? The only files that need to change are sam_
On Tue, Aug 23, 2011 at 6:17 PM, shashi shekhar wrote:
> Hi,
>
>
> Iis it possible to add own visualization tool in galaxy?
>
>
>
>
> On Tue, Aug 23, 2011 at 5:55 PM, Daniel Blankenberg wrote:
>
>> Hi Shashi,
>>
>> Have a look at:
>> http://wiki.g2.bx.psu.edu/Admin/Tools/External%20Display%20App
Hi,
In Galaxy there is visualization option .how it works .Are documents are
available for visualization tool.
Thanks for Reply
Regards
shashi
On Tue, Aug 23, 2011 at 5:55 PM, Daniel Blankenberg wrote:
> Hi Shashi,
>
> Have a look at:
> http://wiki.g2.bx.psu.edu/Admin/Tools/External%20D
We are in need of a galaxy upgrade (we missed the last galaxy-dist update at
the end of June). However, we don't want to update to a 2 month old release
only to have a new release come out shortly after. Could someone on the
development team give me an estimate of when the next galaxy-dist upda
Hi Shashi,
Have a look at:
http://wiki.g2.bx.psu.edu/Admin/Tools/External%20Display%20Applications%20Tutorial
And at the XML files in the directory: $GALAXY_ROOT/display_applications/
Thanks for using Galaxy,
Dan
On Aug 23, 2011, at 7:30 AM, shashi shekhar wrote:
> Hi All,
>
>
> I want
On 08/23/2011 03:47 AM, Peter Cock wrote:
On Mon, Aug 22, 2011 at 5:29 PM, Samuel Lampa
wrote:
Hi,
I'm trying to parse the XML toolconfig format, for generating a lightweight
command config wizard in an Eclipse based product.
I wonder: Boolean parameters for some tools (such as the emboss/te
Hi All,
I want to add my own Visualization tool in local instance of galaxy .how
i will do it in galaxy ? i want to integrate jmol in galaxy.
Regards
shashi
___
Please keep all replies on the list by using "reply all"
in your mail clien
I'm glad it worked Chris, I'm keeping thread on the mailing list for
future reference...
Original Message
Subject: Re: [galaxy-dev] DRMAA broken following SGE update. How to fix?
Date: Tue, 23 Aug 2011 11:56:13 +0100
From: Chris Cole
Organization: University of Dundee
To: Roman
Hi Brad,
I managed to do a git script to select out the GFF code and tests from
your bcbb repository and get it into the Biopython source tree. The
folder changes made it interesting ;)
Input: https://github.com/chapmanb/bcbb (master branch)
Output: https://github.com/peterjc/biopython/tree/brad
Hi Chris,
Take a look at this file :
lib/galaxy/jobs/runners/drmaa.py
in your galaxy directory.
You can export a path for binaries here. For example :
export PATH=$PATH:/opt/bin/
before export PYTHONPATH
Moreover, do not forget other path values in your service script or in your
galaxy user pro
Did you adjust the SGE_ROOT environment variable to point to the
libdrmaa for SGE (probably /opt/sge_62u5_gr/bin/lx24-amd64) ?
This is of course just a guess, could you please provide some error
messages/logs ?
Cheers,
Roman
On 2011-08-23 10:20, Chris Cole wrote:
> BUMP
>
> Does anyone have any
BUMP
Does anyone have any idea on this? Our Galaxy is currently out of action
until this is sorted.
Thanks,
Chris
On 22/08/11 10:08, Chris Cole wrote:
Hi,
Following a recent update to our SGE, DRMAA is failing to load in
galaxy. The reason being that the path has changed. How do I change th
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