files.
regards, Andreas
On 22.05.2013 13:57, Dannon Baker wrote:
On Wed, May 22, 2013 at 3:12 AM, Andreas Kuntzagk
mailto:andreas.kuntz...@mdc-berlin.de>> wrote:
But how do I get the workflow_id? For example for the workflow
https://main.g2.bx.psu.edu/u/__gm2123/w/cloudmap-unmapped-__muta
.)
regards, Andreas
-Dannon
On Tue, May 21, 2013 at 11:56 AM, Andreas Kuntzagk
mailto:andreas.kuntz...@mdc-berlin.de>> wrote:
Hi,
I want to make workflows published on usegalaxy.org <http://usegalaxy.org>
available for users
on our local instance. How do
Hi,
I want to make workflows published on usegalaxy.org available for users on our local instance. How
do I do this?
regards, Andreas
--
Andreas Kuntzagk
SystemAdministrator
Berlin Institute for Medical Systems Biology at the
Max-Delbrueck-Center for Molecular Medicine
Robert-Roessle-Str
style I would write
"
...
...
"
But where do I put the "-l h_vmem"?
regards, Andreas
--
Andreas Kuntzagk
SystemAdministrator
Berlin Institute for Medical Systems Biology at the
Max-Delbrueck-Center for Molecular Medicine
Robert-Roessle-Str. 10, 13125 Berlin, Ge
"?
regards, Andreas
--
Andreas Kuntzagk
SystemAdministrator
Berlin Institute for Medical Systems Biology at the
Max-Delbrueck-Center for Molecular Medicine
Robert-Roessle-Str. 10, 13125 Berlin, Germany
http://www.mdc-berlin.de/en/bim
HERE history_dataset_association.id =
%(param_1)s' {'param_1': u'e96c6ce43a3d239a'}
Looks like the id for the dataset is wrong. How can this happen and how can I
fix this?
regards, Andreas
--
Andreas Kuntzagk
SystemAdmi
in __str__
return getattr(self, mainMethName)()
File "cheetah_DynamicallyCompiledCheetahTemplate_1354790596_63_67504.py",
line 84, in respond
NotFound: cannot find 'files_path' while searching for 'input.files_path'
Andreas
On 06.12.2012 10:52, Andreas Kuntzagk
Sorry, I think I had not really restarted galaxy after making the change.
After I changed some logging options in universe_wsgi.ini and restarted it's
suddenly working.
So I can confirm your fix works.
Thank you for your help.
Andreas
On 05.12.2012 13:40, Andreas Kuntzagk wrote:
Hi,
9:30 AM, Andreas Kuntzagk
wrote:
I see that this issue came up before by Oleksandr Moskalenko in October but was
unresolved then.
Is there a workaround now?
regards, Andreas
The velvet wrapper is not going to be usable for real user jobs until someone
rewrites it to work without d
I see that this issue came up before by Oleksandr Moskalenko in October but was
unresolved then.
Is there a workaround now?
regards, Andreas
On 29.11.2012 11:47, Andreas Kuntzagk wrote:
Hi,
I enabled velvet on our local install. But when I try to use velveth, I get an
"Permission d
t_27903_dat
regards, Andreas
--
Andreas Kuntzagk
SystemAdministrator
Berlin Institute for Medical Systems Biology at the
Max-Delbrueck-Center for Molecular Medicine
Robert-Roessle-Str. 10, 13125 Berlin, Germany
http://www.mdc-berlin.de/en/bimsb/BI
t me at the input sequences for this run,
so that I can try
running this via the console, and see if there's something happening in lastz
that I don't understand?
Bob H
On Nov 26, 2012, at 3:35 AM, Andreas Kuntzagk wrote:
Hi,
I just noticed that this was another case of a tool
Please ignore this. You can move it to a different section.
Andreas
On 27.11.2012 13:19, Andreas Kuntzagk wrote:
Hi,
In the past I installed bwa_wrapper from the toolshed. Unfortunately I must
have choosen a wrong
category. Currently it is not part of any tool section. According to
name and a different id:
I tried to rectify this by deleting and reinstalling but unfortunately there is no way to really
reinstall and it always ends up with the same problem again.
Is there a way to really uninstall?
regards, Andreas
--
Andreas Kuntzagk
SystemAdministrator
Berlin Inst
Hi Peter,
thanks for your replies.
On 27.11.2012 11:44, Peter Cock wrote:
On Tue, Nov 27, 2012 at 10:38 AM, Andreas Kuntzagk
wrote:
Dear Peter,
As the author of several tool wrappers, I've been asking for a Galaxy
wide mechanism for Galaxy to tell the tool how many threads it can
use
galaxy-dev-boun...@lists.bx.psu.edu] Namens Andreas Kuntzagk Verzonden:
dinsdag 27
november 2012 9:58 Aan: Bob Harris CC: galaxy-dev@lists.bx.psu.edu Onderwerp:
Re: [galaxy-dev]
multithreaded tools
Hi,
the four processes I saw where all called "lastz" and ran in parallel and
consu
ssion
to request that many slots/CPUs.
A list of all these wrappers on the Wiki would be nice.
regards, Andreas
--
Andreas Kuntzagk
SystemAdministrator
Berlin Institute for Medical Systems Biology at the
Max-Delbrueck-Center for Molecular Medicine
Robert-Roessle-Str. 10, 13125 Berlin, Germany
Howdy, Andreas,
The four processes started for a galaxy lastz job must involve post-processing
the lastz output
through some other shell tool. Lastz by itself doesn't support multiple
threads or processes.
Bob H
On Nov 26, 2012, at 3:58 AM, Andreas Kuntzagk wrote:
Hi,
I'm wande
Hi,
I'm wandering how galaxy supports tools that are multithreaded or multi-process.
When working with lastz I noticed that it starts 4 parallel processes.
Is that always so? Can this be adjusted? What other tools also are
multi-process?
regards, Andreas
--
Andreas Kun
Hi,
I just noticed that this was another case of a tool that needs more then the 1GB memory that is
default on our cluster. After adjusting the job_runner settings everything seems fine.
regards, Andreas
On 15.11.2012 09:08, Andreas Kuntzagk wrote:
Hi,
when I start a lastz job it submits a
Hi,
I upgraded to the latest version and again some tools moved to tool_shed. I now need to set job
runners for these tools. Is there an easy way to get the tool_ids other then hovering the mouse over
the tool name and write down the id?
regards, Andreas
--
Andreas Kuntzagk
TP/1.1"
200 - "http://bbc.mdc-berlin.de/galaxy/history"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:16.0)
Gecko/20100101 Firefox/16.0"
galaxy.jobs.runners.drmaa INFO 2012-11-15 09:03:11,553 (254) queued as 1282605
galaxy.jobs.runners.drmaa DEBUG 2012-11-15 09:03:
Ok, I've found the solution. sam_fa_indices.loc contained relative paths. When I changed to absolute
paths it worked.
regards, Murple
On 02.11.2012 09:26, Andreas Kuntzagk wrote:
Oh,
I forgot to mention it:
hg18.fa.fai is already in tool-data/shared/ucsc/hg18/sam_index/ as a link to
:59:24.000, Andreas Kuntzagk wrote:
Dave,
In the meantime I found that out by myself howto generate the FASTA and
also to rum "samtools faidx" on it. The info about "all_fasta.loc" was
missing. But it's still not working.
Let me summarize what I did so far:
- tool-data/s
an be added to the page you are mentioning.
On Thu, Nov 1, 2012 at 4:27 AM, Andreas Kuntzagk
wrote:
Hi,
thank you for the pointer.
I was only looking at this wiki page:
http://wiki.g2.bx.psu.edu/Admin/Data%20Integration
Maybe this should point to your page?
regards, Andreas
On 31.10.2012
uld recommend
downloading the relevant .2bit file and converting it back to FASTA with
twoBitToFa, then updating
your all_fasta.loc file to point to the resulting .fa file.
--Dave B.
On 11/1/12 06:27:49.000, Andreas Kuntzagk wrote:
Hi,
It's still not working. I just noticed that the sam
n Wed, Oct 31, 2012 at 11:30 AM, Andreas Kuntzagk
wrote:
Hi,
I'm still setting up a local galaxy. Currently I'm testing the setup of NGS
tools. If I try "SAM to BAM" for a BAM file that has "hg18" set as build I
get a message that
"Sequences are not currently ava
Hi,
thank you for the pointer.
I was only looking at this wiki page:
http://wiki.g2.bx.psu.edu/Admin/Data%20Integration
Maybe this should point to your page?
regards, Andreas
On 31.10.2012 17:50, Carlos Borroto wrote:
On Wed, Oct 31, 2012 at 11:30 AM, Andreas Kuntzagk
wrote:
Hi,
I'm
o add one line for each build*tool combo? These lines seem very redundant to me.
--
Andreas Kuntzagk
SystemAdministrator
Berlin Institute for Medical Systems Biology at the
Max-Delbrueck-Center for Molecular Medicine
Robert-Roessle-Str. 10, 13125 Berlin, Germany
http://www.mdc-b
My fault. I did not set a title for it.
(Anyway this should be caught I think.)
regards, Andreas
On 25.10.2012 13:18, Andreas Kuntzagk wrote:
Hi,
on our local Galaxy instance I try to setup Visualization.
I followed
http://wiki.g2.bx.psu.edu/Learn/Visualization#Setup_for_Local_Instances
But
fire_replace_event
value = ext.set(state, value, previous, initiator or self)
File
'/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py',
line 847 in set
new_state, new_dict = instance_state(child), instance_dict(child)
AttributeError:
In the main toolshed I find bam_to_bigwig 2 times.
Description, Version and Requirements seem the same.
How am I to decide which one to use?
regards, Andreas
--
Andreas Kuntzagk
SystemAdministrator
Berlin Institute for Medical Systems Biology at the
Max-Delbrueck-Center for Molecular Medicine
Cluster
NH INBRE Grid
Computational Genetics Lab
Dartmouth College, HB 6223
L24 Berry/Baker Library
Hanover, NH 03755
Phone: 603-646-8109
http://discovery.dartmouth.edu
http://columbia.dartmouth.edu/grid
http://www.epistasis.org
*
This body part will be downloaded on demand.
--
A
'dataset'.
What is the problem here?
regards, Andreas
--
Andreas Kuntzagk
SystemAdministrator
Berlin Institute for Medical Systems Biology at the
Max-Delbrueck-Center for Molecular Medicine
Robert-Roessle-Str. 10, 13125 Berlin, Germany
http://www.mdc-berlin.de/en/bimsb/BI
of galaxy involved so I'm
sure there are some bugs.
regards, Andreas
On 29.03.2012 16:12, Andreas Kuntzagk wrote:
Hi,
Ok, I was digging around for this and it seems to be a bit more involved then I
expected.
Problem is I don't really understand the interplay of DRMAAJobRunne
Hi,
Ok, I was digging around for this and it seems to be a bit more involved then I
expected.
Problem is I don't really understand the interplay of DRMAAJobRunner and the
user management.
Can somebody provide me with some pointers?
regards, Andreas
On 28.03.2012 13:30, Andreas Kuntzagk
users. For unknown users I just continue to use the
"galaxy" user. I guess a good starting point would be DRMAAJobRunner.queue_job
Do you see any bigger problems coming my way?
How best do I avoid to degress from the main tree to much?
regards, Andreas
On 27.03.2012 09:57, Andreas
On 20/03/12 16:31, Andreas Kuntzagk wrote:
Hi,
I (re-)installed galaxy on our server and managed to set it up to run jobs
through our cluster (GridEngine). It's also running behind an Apache proxy now.
But now I'm wondering how to setup to have the cluster jobs run as the real
c
(otherwise, they will have to
# be created by an admin).
#allow_user_creation = True
# Allow administrators to delete accounts.
#allow_user_deletion = False
# Allow administrators to log in as other users (useful for debugging)
#allow_user_impersonation = False
regards, Andreas
--
Andreas Kuntzag
is topic a little thin.
We use NIS for managing users and passwords across the cluster. How do I
connect that to Galaxy?
regards, Andreas
--
Andreas Kuntzagk
SystemAdministrator
Berlin Institute for Medical Systems Biology at the
Max-Delbrueck-Center for Molecular Medicine
Robert-Roessle-Str.
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