Hi all,
I have exactly the same problem as described here:
http://gmod.827538.n3.nabble.com/Job-output-not-returned-from-cluster-td879580.html
All the SGE stuff is administrated in our company and unfortunately they know
nothing about
Galaxy and so it?s my task to get it running.
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?
Thanks in advance!
Cheers,
Sascha
___
-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Sascha Kastens
Sent: Monday, July 09, 2012 11:26 AM
To: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Job output not returned from Cluster
Hi!
Unfortunately I was not able to fix this problem yet
] Job output not returned from Cluster
Sent:
Freitag, 13. Juli 2012 19:35
From:
Nate Coraor (n...@bx.psu.edu)
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
Hi Dev-Team,
are you planning or maybe working on an update which enables the
possiblilty to run workflows in batch mode with paired end data?
Cheers,
Sascha
___
Please keep all replies on the list by using reply all
in your mail
of the
workflow is a deinterlacing of the datafiles.
The script is available here:
http://geertvandeweyer.zymichost.com/index.php?page=readid=27
Best Regards,
Geert
On 07/18/2012 02:38 PM, Sascha Kastens wrote:
Hi Dev-Team,
are you planning or maybe working on an update which enables the
possiblilty
Hi!
Yeah, it seems that there is now way to request the API key automatically.
One simple apporach would be an extra text input field where the user has
to enter his or her API key.
In my use case it will be better to use a file for mapping $__user_id__ -
api_key.
We run Galaxy only
to
access the key. It would also be a good idea to add some checking for e.g. a
logged in user and that the user has an API key set.
Thanks for using Galaxy,
Dan
On Jul 19, 2012, at 5:52 AM, Sascha Kastens wrote:
Hi!
Yeah, it seems that there is now way to request the API key
:
default_cluster_job_runner = drmaa://-pe make 16 -q bioinf.q/ this submits the
job to our bioinf-cluster
on a node with 16 free slots. So you should check how you submit jobs via
commandline with PBS and use
these paramaters for setting drmaa:///
Cheers,
Sascha Kastens
Project Manager
GATC Biotech AG
Jakob
?].iteritems():
wf_data[?ds_map?][step_id] = {?src?:?ld?, ?id?:ds[?id?]}
What I am seeking for is something like this:
wf_data[?ds_map?][step_id] = {?src?:?local?, ?path?:?path/to/file?}
Cheers,
Sascha Kastens
Project Manager
GATC Biotech AG
Jakob-Stadler-Platz 7
D-78467 Konstanz
for uploading
files into a library so it would be nice if you can give me a hint.
With this information I should be able to extend the normal upload
tool.
Thanks in advance!
Cheers,
Sascha Kastens
Project Manager
GATC Biotech AG
Jakob-Stadler-Platz 7
D-78467 Konstanz
Phone: +49
is, that Galaxy copies the files pointed to
into it?s database directory
which results in the former problem of space overhead. Is there a way to let
Galaxy only copy the links?
Thanks in advance,
Sascha Kastens
Project Manager
GATC Biotech AG
Jakob-Stadler-Platz 7
D-78467 Konstanz
Hi!
This might be helpful:
http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies
Cheers,
Sascha
Original Message
processed by CONSOLIDATE
Subject:
[galaxy-dev] How to configure samtools in galaxy on cluster
Sent:
Montag, 6. August 2012 19:39
From:
michael xu
Hi all,
I?m running a local instance of Galaxy and every time I start it, Galaxy tries
to recover some jobs. These jobs are not running anymore and I get the following
information:
galaxy.jobs DEBUG 2012-08-07 10:58:08,056 (418) Working directory for job is:
Ahhh, of course! Thanks David. I have missed this entry somehow o_O
Cheers
Original Message
processed by CONSOLIDATE
Subject:
RE: [galaxy-dev] Job recovery of non existing job
Sent:
Dienstag, 7. August 2012 11:38
From:
David Roquis (david_roq...@hotmail.com)
Hi Sascha,
Can you see
Hi all!
I have two questions about histories in Galaxy:
1. Is it possible to mark/set a history as published via the API?
2. How can I get the ID of the current users history via a tool? Something like
${__app__.model.User.get($__user_id__).histories[0].id} ?!
Thanks in
!
Cheers,
Sascha
Original Message
processed by CONSOLIDATE
Subject:
[galaxy-dev] Some questions about histories
Sent:
Dienstag, 14. August 2012 12:10
From:
Sascha Kastens (s.kast...@gatc-biotech.com)
Hi all!
I have two questions about histories in Galaxy:
1. Is it possible
)
On Aug 15, 2012, at 10:08 AM, Sascha Kastens wrote:
Hi again!
I was able to implement a quite dirty solution:
first I edited /lib/galaxy/model/mapping.py and extended
assign_mapper( context, User, User.table,
properties=dict( histories=relation( History, backref=user
Hi all!
I am facing a simple problem but can?t find a solution to solve it.
Before I start describing my problem here is the code from my tool:
conditional name=sReference
param name=reference type=select label=Select a reference genome
help=
option value=mm9_64mm9_64/option
=select based on former selection
Sent:
Dienstag, 4. September 2012 12:56
From:
Hans-Rudolf Hotz (h...@fmi.ch)
Hi Sascha
I don?t quite understand your question...
$sReference.ref is the variable you are looking for, isn?t-it?
Regards, Hans
On 09/04/2012 11:40 AM, Sascha Kastens wrote:
Hi
Hi all!
The accordion style would be very nice for me and my user base.
Cheers,
Sascha
Original Message
processed by CONSOLIDATE
Subject:
Re: [galaxy-dev] Tool Menu Behavior
Sent:
Donnerstag, 11. Oktober 2012 23:44
From:
Jeremy Goecks (jeremy.goe...@emory.edu)
Carrie,
Currently,
Hi all!
I have a tool which takes one ore more input files. For each input file one
output is created,
i.e. 1 input file - 1 output file, 2 input files - 2 output files, etc.
What is the best way to handle this? I used the directions for handlin multiple
output files where
the ?Number
Hi devs!
After updating my local instance to changeset
19cbbaf566216cb46ecc6a6d17e0f1e0ab52978e my tool which submits a workflow via
the
API and set force_history_refresh to TRUE does not refresh the history anymore.
The job is submit via DRMAA to SGE. Unfortunately the job seems to run
Hey devs!
It seems that many things related to history datasets has changed since I have
updated my local Galaxy instance and
the current version.
Unfortunately it seems that one cannot Display data in browser (eye icon) if
the dataset is in error state. Where can I
get that feature
Eberhard (carlfeberh...@gmail.com)
Hi Sascha,
This may be due to the recent history panel changes. Can you update to the
latest revision and see if the error still occurs?
Thanks,
Carl
On Tue, Nov 20, 2012 at 2:22 AM, MSc. Sascha Kastens
s.kast...@gatc-biotech.com wrote:
Hi devs!
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