On Thu, Oct 10, 2013 at 8:20 PM, Nate Coraor n...@bx.psu.edu wrote:
Hi all,
The recent changes to the DRMAA runner are for better handling
of job-ending conditions under slurm, but it looks like SGE has
different behavior when a job finishes. I'll provide a fix for this
shortly, in the
On Thu, Oct 10, 2013 at 10:00 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Wed, Oct 9, 2013 at 10:01 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Am Mittwoch, den 09.10.2013, 19:15 +0100 schrieb Peter Cock:
On Tue, Oct 8, 2013 at 9:57 PM, Dave Bouvier
On Thu, Aug 1, 2013 at 8:43 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
As of 10290:d34d6d1da813, nsltradamus and effectivet3 should start returning
valid test results. As for seq_rename, ...
--Dave B.
Hi Dave,
That fix is on galaxy-central and the Test Tool Shed, and my tests
have
This sounds like a good way to solve the problem, I guess I would modify
On Thu, Oct 10, 2013 at 6:10 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Dear all,
some SGE instances will add automatically an semicolon add the end of
each command, resulting in a disrupted
Hi Björn,
Are you certain that SGE is responsible? I ran in to the same thing with
bowtie2 with other runners. The double semicolon is invalid syntax in
Bourne-compatible shells and so the tool ought to be fixed not to produce them
(it happens under certain combinations of options). Have
Opps, sent that last e-mail before I meant to, gmail is acting very
buggy for me this morning. I just meant to say I would modify
build_command_line in lib/galaxy/jobs/runners/__init__.py instead. It
seems like there is a lot of logic in there for this kind of thing
already. I will create a
The paster script distributed with Galaxy is a stripped down Galaxy
specific version. It only supports the command serve and the arguments
--daemon or --reload.
--
James Taylor, Associate Professor, Biology/CS, Emory University
On Fri, Oct 11, 2013 at 8:36 AM, Renato Alves
Il giorno ven, 11/10/2013 alle 01.10 +0200, Björn Grüning ha scritto:
Dear all,
some SGE instances will add automatically an semicolon add the end of
each command, resulting in a disrupted job, because ';;' are not
allowed.
The latest changes to the Bowtie2 wrapper resulting in such a
Hi Nicola,
interesting you fixed bowtie in the same way than we did. But somehow I
would like to strip a trailing ';' by default in Galaxy, when it does
not break anything else.
Thanks for sharing!
Bjoern
Il giorno ven, 11/10/2013 alle 01.10 +0200, Björn Grüning ha scritto:
Dear all,
Ah now I got it ... there are two build_command_line functions.
lib/galaxy/tools/__init__.py and lib/galaxy/jobs/runners/__init__.py.
And one is adding a trailing ';'
So either stripping the trailing semicolon, right after creating the
command line from cheetah (patch was attached) or adding
Hi Nate,
Hi Björn,
Are you certain that SGE is responsible? I ran in to the same thing with
bowtie2 with other runners.
The double semicolon is invalid syntax in Bourne-compatible shells and so the
tool ought to be fixed not to produce them (it happens under certain
combinations of
My plan is to refactor build_command_line out of
lib/galaxy/jobs/runners/__init__.py, into its own module and add unit
tests for this functionality. I'll issue a pull request and let people
test it. I am also testing Nicola's PR, I will approve it shortly.
Nate yelled at me for committing code
I already fixed it one week ago:
https://bitbucket.org/nsoranzo/galaxy-central-tools/commits/74b5fd2318d33b76382b052eae6a28b035dc075f
but then Ross committed a similar fix to galaxy-central, I merged it in
my pull request and then Ross reverted the fix!
This is the reason for rebasing pull
Hello,
I'm working in the university of Lausanne. We are currently working
with fire ants, Solenopsis invicta.
I was wondering if that would possible to upload Solenopsis invicta's
genome on the Galaxy platform, which could be very useful to us and
certainly to other people.
Thank you !
Heya, Andy
Galaxy hasn't been designed to be loaded in an iframe yet.
Currently, the javascript in Galaxy makes use of the window variable top -
which points to the highest browser window in the DOM. There are many
instances where we rely on both 'top' and the link target '_top' to control
the
Hi Patrick,
I think this is worth consideringand will run by team. Genomes are a bit
on hold right now due to the move of the public server, but once that
resumes, I have a ticket going with public requests in it. Would you
please send me the details for this organism: exact accession(s),
On 9/12/13 10:35 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
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
Am Freitag, den 11.10.2013, 09:18 -0500 schrieb John Chilton:
My plan is to refactor build_command_line out of
lib/galaxy/jobs/runners/__init__.py, into its own module and add unit
tests for this functionality. I'll issue a pull request and let people
test it. I am also testing Nicola's PR, I
Hey All,
Patch available with test case, let me know what I broke :).
https://bitbucket.org/jmchilton/galaxy-central-multi-input-tool-fixes-2/commits/e0016057e1648d7f4d29fbaf14252cbefff6d0bd
-John
On Fri, Oct 11, 2013 at 10:37 AM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
I've managed to resolve this issue. I'm not sure how I ended up with this
issue, but in case anyone else get's hit by it, here's what I've learned:
-At version 0.6, SQLAlchemy changed the format for connecting to postgresql:
[postgresql] The postgres dialect is now named postgresql
-I
Hello!
This is more or less a repost of (several) previously unanswered
questions. Sadly it seems that one does generally not recieve an
answer to this topic:
http://lists.bx.psu.edu/pipermail/galaxy-user/2011-October/003400.html
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