On 10/17/2014 10:39 AM, Peter Cock wrote:
On Thu, Oct 16, 2014 at 11:05 PM, Wolfgang Maier
wolfgang.ma...@biologie.uni-freiburg.de wrote:
Hi,
this is just to make sure: the GALAXY_SLOTS environmental variable set by
Galaxy when running tools will always be a number = 1 with 1 being the
default
On 10/17/2014 02:47 PM, John Chilton wrote:
In theory GALAXY_SLOTS is now always set unless Galaxy is pretty old -
I still think it is important for tools to specify defaults using the
\${GALAXY_SLOTS:-4} idiom so that tools themselves don't have explicit
dependencies on the Galaxy runtime and
Hi,
this is just to make sure: the GALAXY_SLOTS environmental variable set
by Galaxy when running tools will always be a number = 1 with 1 being
the default if nothing else is configured in the job runner settings ?
Correct ?
Thanks,
Wolfgang
appear to have a user name. Any
clue how that happened? Do all newly created workflows have that same
issue with your Galaxy instance?
Sorry I have not been of more help.
-John
On Sun, Oct 12, 2014 at 10:50 AM, Wolfgang Maier
wolfgang.ma...@biologie.uni-freiburg.de wrote:
Dear all,
our local
clue how that happened? Do all newly created workflows have that same
issue with your Galaxy instance?
Sorry I have not been of more help.
-John
On Sun, Oct 12, 2014 at 10:50 AM, Wolfgang Maier
wolfgang.ma...@biologie.uni-freiburg.de wrote:
Dear all,
our local Galaxy does not seem to be able
On 13.10.2014 14:23, Dannon Baker wrote:
On Mon, Oct 13, 2014 at 8:14 AM, John Chilton
jmchil...@gmail.com
mailto:jmchil...@gmail.com wrote:
My understanding is that it was briefly optional (and maybe just
through the API) but that was a bug. I think Dannon made that fix a
few
Dear all,
our local Galaxy does not seem to be able to export workflows anymore,
instead fails with, for example:
Not Found
The resource could not be found.
No route for /u/w/myworkflow/json-download
We are running latest_2014.10.06 .
Has anyone else experienced this ?
Thanks,
Wolfgang
On 28.07.2014 12:22, Peter Cock wrote:
This is standard behaviour to prevent special characters being used
to construct malicious command lines. It can be configured within
your tool definition using the sanitizer tag set:
Thanks a lot for all the encouraging feedback.
More than anything else the friendly atmosphere that seems to prevail on
this mailing list makes me think that it may indeed be worthwhile to
make the package available to this community !
I will have a closer look at the toolshed instructions and
Dear all,
I am maintaining a (still young) suite of command line tools (written in
Python) for identification of mutations in model organism genomes
through whole-genome sequencing (https://sourceforge.net/projects/mimodd/).
MiModD aims at geneticists that do not have much background in
if possible please?
Thanks
Neil
Message: 3
Date: Fri, 30 May 2014 15:04:47 +0200
From: Wolfgang Maier wolfgang.ma...@biologie.uni-freiburg.de
To: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] stdout in history
Message-ID: lm9vle$70e$2...@ger.gmane.org
Content-Type: text/plain; charset=UTF-8; format
you could just redirect stdout to /dev/null in the tool's xml command
line ?
Is that an option for you ?
Cheers,
Wolfgang
On 30.05.2014 14:35, neil.burd...@csiro.au wrote:
Hi,
It seems that the first 4/5 lines that are printed in the source
code tools appear in the history (when
, ...) by hand not use the
CloudMap pipeline on Drosophila?
Thanks
From: Wolfgang Maier
[wolfgang.ma...@biologie.uni-freiburg.de]
Sent: Friday, February 14, 2014 11:48 AM
To: Wang, Xiaofei
Cc: galaxy-dev@lists.bx.psu.edu
Subject: RE: [galaxy-dev
Last time I checked the EMS Variant Density Mapping tool, specifically, had
an unnecessary restriction to chromosome names as in WS220.64 (chrI, chrII,
chrIII, chrIV, chrV, chrX). So maybe before putting too much effort into the
SnpEff side of the workflow, maybe try the Mapping tool individually
Dear all,
in one of my tools I'm populating a list of possible
choices from a file in the history using the options
from_dataset tag.
Now using the tool as part of a workflow, the choices are
not calculated at the setup stage, but I have to enter
free-text and Galaxy seems to evaluate whether
15 matches
Mail list logo
