On Wed, Dec 4, 2013 at 4:21 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Mon, Dec 2, 2013 at 3:37 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Sun, Dec 1, 2013 at 7:10 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Great. I'll probably merge the c25 branch
Il 2013-12-04 20:48 Jim Johnson ha scritto:
On 12/4/13, 10:21 AM, Peter Cock wrote:
On Mon, Dec 2, 2013 at 3:37 PM, Peter Cock
p.j.a.c...@googlemail.com [1] wrote:
On Sun, Dec 1, 2013 at 7:10 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de [2] wrote:
Great. I'll probably merge
Peter Cock wrote:
I've been working on this using JJ's work on column picking
in the BLAST XML to tabular tool - viewable here:
...
I'm considering splitting the column picker into three, the
standard 12 columns, the further 13 used in our extended
25 column output, and a third category
Hi, Galaxy-Developers,
I apologize if this question has been answered before; I'm trying to
override a couple of environment variables on a per-tool level, for a tool
that is not installed in the toolshed. I've read a post on the mailing
list that suggests this is possible for tools installed
Hi John,
It works very fine. Thank you again for your help, very useful :).
Have a nice day,
Mish
From: mish...@hotmail.com
To: chil...@msi.umn.edu
Date: Mon, 2 Dec 2013 08:51:28 +
CC: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Galaxy code: data libraries
Hi John,
Thank
I have installed the ngsplot galaxy tool from http://code.google.com/p/ngsplot.
This tool creates a set of three pdf files. In older versions of Galaxy, the
tool ran correctly with no problems. A recent update broke the tool. The job
runs but is unable to finish. Here is the error
Hi David, hi all!
I have a similar/the same issue in another setting...
galaxy/galaxy_dist/lib/galaxy/jobs/runners/local.py, line 116, in queue_job
job_wrapper.finish( stdout, stderr, exit_code )
[...]
David, Christian,
Very sorry about this - this is probably related to fixing some other
errors -
http://dev.list.galaxyproject.org/Unicode-in-tool-stderr-crashing-galaxy-tt4661749.html#a4661750.
I will try to look into this.
Christian - what database are targeting? Is it MySQL as well?
David -
Actually, can you verify that this commit
https://bitbucket.org/galaxy/galaxy-central/commits/e786022dc67ed918050bd81b9ac679ac958e4f75
is in your distribution and if it is try changing:
DEFAULT_ENCODING = 'utf-8'
in lib/galaxy/util.py to
DEFAULT_ENCODING = 'latin-1'
If that works then - I can
My version is 11216:c458a0fe1ba8. Does this cover the commit?
On Dec 5, 2013, at 12:32 PM, John Chilton wrote:
Actually, can you verify that this commit
https://bitbucket.org/galaxy/galaxy-central/commits/e786022dc67ed918050bd81b9ac679ac958e4f75
is in your distribution and if it is try
Looks to yes...
% hg contains -c c458a0fe1ba8 e786022dc67ed918050bd81b9ac679ac958e4f75
lookup for revision 'e786022dc67ed918050bd81b9ac679ac958e4f75' yields
changeset 10953:e786022dc67e
true
You could also verify lib/galaxy/jobs/__init__.py contains the import
from galaxy.util import unicodify.
Right, nevermind, 'hg log' listed that changeset 10953:e786022dc67e.
Changing DEFAULT_ENCODING to 'latin-1' in lib/galaxy/util/__init__.py worked.
Do I need to alter ALL the MySQL tables to UTF-8, or just a selection of
tables? Will future updates explicitly create new tables with
Hi Valeria,
Please always replay-all to keep email threads on the original list.
Your setting for tool_dependency_dir should not be as you've stated:
tool_dependency_dir = tool_dependencies
It should be an actual path on your local file system, something like:
tool_dependency_dir =
Fantastic!
For this particular problem - I guess you don't strictly need to
modify more than just job and maybe task tables. I suspect at some
point there will be a non-latin-1 job parameter or history name or
username, etc... that will result in a similar problem though - so if
you could just
John,
I stopped galaxy, then ran ALTER DATABASE galaxydb DEFAULT CHARACTER SET =
'utf8', then ran ALTER TABLE `[table]` DEFAULT CHARACTER SET = 'utf8' on all
the tables in galaxydb. After starting up galaxy and rerunning the jobs (using
the unaltered version of lib/galaxy/util/__init__.py),
Hello, Karen
This is a bug and I wanted to let you know I'm looking into it now:
https://trello.com/c/dzBmbyqF
Sorry for the frustration and thanks for the report,
Carl
On Mon, Dec 2, 2013 at 6:23 PM, Karen Miga khm...@soe.ucsc.edu wrote:
Hello,
I am trying to use phyloviz on the
What happens if you choose Reset to install from the Repository Actions
menu? You should be presented with a page that shows the repository as
uninstalled, at which time you can attempt to install it again.
On Dec 5, 2013, at 3:11 PM, Valeria Parreira Pinto vparr...@uoguelph.ca wrote:
Hi
Click on the Admin option from the top menu bar, then click on the Mange
installed tool shed repositories. The find the s_mart repository from that
page and clck on it. The from the Repository Actions menu, select Reset to
install or Repair repository if it is available.
On Dec 5, 2013, at
Hmmm... can you try adding ?charset=utf8 to your database connection
string - that may fix the problem?
If not - is there a way to tell if the actual columns have changed.
Some comments on stackoverflow make it sound like the commands you
listed will only affect new columns.
Can you try the
Hi,
I know that if I put :
${ __app__.model.User.get( $__user_id__ ).api_keys[0].key }
in my tools xml file I am able to get the current api key.
The xml calls my python script with this value, which i then use to execute
workflows via the API.
However, if this is value empty/blank is
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