Hi all,
I think I've found a bug in the Galaxy test framework :(
With most file inputs, a gzipped input file works fine (Galaxy's upload code
handles unzipping it). However, with multiple=true this seems to break
(with the Twill backend, the API test framework is OK), e.g.
param name=filenames
This is a new one for me. What configuration are you using for both your
'database_connection', and the 'amqp_internal_connection' in your
universe_wsgi.ini?
On Fri, Jun 13, 2014 at 12:29 AM, xlwang xlwang_0...@163.com wrote:
Hello,
when i run my galaxy instance type:
$ sh run.sh
I get
Hi Jun,
You should be using Tool Data Tables instead of acting on .loc files directly.
You can specify a data table to be built up from more than one file and
multiple data tables to use various file configurations.
‘from_data_table’:
Hi Nate,
we encountered an addition bug related to the object-store:
Traceback (most recent call last):
File /usr/local/galaxy/galaxy-
dist/lib/galaxy/jobs/runners/__init__.py, line 153, in prepare_job
job_wrapper.prepare()
File /usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py,
I am writing a tool that should be configurable by the server admin. I am
considering adding a configuration file, but where should such a file be
placed? Is the tool-data directory the right place? Is there another
standard way for per-tool configuration?
Jan
I would have different answers for your depending on what options are
available to the server admin. What exactly about the tool is
configurable - can you be more specific?
-John
On Fri, Jun 13, 2014 at 10:59 AM, Jan Kanis jan.c...@jankanis.nl wrote:
I am writing a tool that should be
Hi all,
When installing and testing the cd-hit tool from jjohnson from the main galaxy
toolshed into my local instance of galaxy, I encountered a problem where galaxy
cannot find the cd-hit program.
The error was:
/bin/sh: 1: cd-hit-est: not found
As I debugged the problem, I found that
The problem seems to be with DRMAA for Python. While it works fine on the
OpenSuse
12.1 box, I'm getting a segfault on RH 6.4.
Surprisingly, the job however gets submitted and run successfully.
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The problem seems to be with DRMAA for Python. While it works fine on the
OpenSuse 12.1 box, I'm getting a segfault on RH 6.4.
Surprisingly, the job however gets submitted and run successfully.
___
Please keep all replies on the list by using
I installed a local instance of galaxy approximately a month ago (build
2014.04.14) and have since updated to latest_2014.06.02. It is running on
64-bit Ubuntu 12.04.
I'm having an issue with the Data Manager to fetch reference genomes
(data_manager_fetch_genome_all_fasta, Rev. 2ebc856bce29).
After multiple restarts of my computer and the galaxy server program, it seems
to have come back so I guess that's solved.
Still can't successfully fetch reference genomes using the data manager but I
guess I should start a new question/thread for that. Gives some dependancy
error about
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Asked this on IRC and was directed to send my request here in case
anyone in the community knows:
I'm looking to find out if anyone has already written tools to manage
installed tools from the toolshed.
E.g. something along the lines of apt-get for
Hi Stephen,
Can you provide the error message from the job? You can look at bug-report for
the the output dataset created by the data manager for the “Data Manager
History (automatically created)” history in your saved histories. Also any
other relevant information from the log would be great
Just for my curiosity, are you running a python environment isolated for galaxy
or just using a system wide python environment?
Regards,
Iyad Kandalaft
Microbial Biodiversity Bioinformatics
Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada
960 Carling Ave.| 960 Ave.
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