Hi all,
I finally resolved the issue I'll mention it here to help anyone else
who has the same issue. In Edit mode on the workflow you add the Workflow
control-Inputs to use the api.
Final question
Everything gets created and stored in the database, but the history column on
the
On Wed, May 8, 2013 at 2:09 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
A technical issue prevented the tests from automatically running. I've
resolved the issue and started a manual run, you should be seeing test
results within 2-3 hours.
--Dave B.
Hi Dave,
As you hoped, these test
On Thu, May 9, 2013 at 10:49 AM, Peter Cock p.j.a.c...@googlemail.com
wrote:
Hi Dave,
As you hoped, these test now shows up on the tool page (as expected
they are test failures - apparently my install script isn't quite right
yet):
...
This one is more interesting, and appears to be a
On Wed, May 8, 2013 at 10:19 PM, Dannon Baker dannon.ba...@gmail.com wrote:
Hey Robert,
I assume this is sqlite? And, when you say you ran this without any
existing database -- was this was a completely new clone of galaxy, or did
you update a prior installation and delete
On Thu, May 9, 2013 at 10:59 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, May 9, 2013 at 10:49 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Dave,
As you hoped, these test now shows up on the tool page (as expected
they are test failures - apparently my install script
On Thu, May 9, 2013 at 11:03 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Wed, May 8, 2013 at 10:19 PM, Dannon Baker dannon.ba...@gmail.com wrote:
Hey Robert,
I assume this is sqlite? And, when you say you ran this without any
existing database -- was this was a completely new clone
Hello all,
I'm exploring a conditional example where I would like to group some
of the select values into a single when clause. Currently it seems
each value requires its own when which leads to duplication and
worse.
For example, I'd like to do something like this:
conditional
On Thu, May 9, 2013 at 12:21 AM, sridhar srinivasan
sridhar2bioi...@gmail.com wrote:
and it is working.. but i could'nt connect to the webpage
http://127.0.0.1:8080/ from another system in same network..
By default, galaxy will only be serving on 127.0.0.1 (localhost), which is
a loopback
Hey Neil,
A user browsing that history wouldn't automatically get the updates (unless
the history was already refreshing for some reason), but they definitely
would upon refresh. Glad you got the rest working!
-Dannon
On Thu, May 9, 2013 at 2:02 AM, neil.burd...@csiro.au wrote:
Hi all,
This isn't an issue with postgresql or mysql; they don't use a temporary
table for table alterations. Can you open up the sqlite database if you
still have it and see what the contents of the migrate_tmp table were?
They'll be a copy of a prior migrated table, I'm just curious what from --
it
Hi,
I uploaded some data and when I click in the eye to see
the data I get the following error. I don't know what can I do to fix
this problem, I trying install some packges from python but didn't solve
my problem. I'm starting think about my operational system, I have
ubuntu 12.04
You can probably use the API for what you want to do, though your users will
need to have an API key to make everything work smoothly. Documentation for the
API is here:
https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html
An alternative approach would be to
Yup, off list by mistake.
-John
On Thu, May 9, 2013 at 8:40 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Off list by mistake?
On Thu, May 9, 2013 at 1:25 PM, John Chilton chil0...@umn.edu wrote:
This is one of the use cases I was trying to address with tool macros. This
has the added
On Thu, May 9, 2013 at 12:56 PM, Dannon Baker dannon.ba...@gmail.com wrote:
This isn't an issue with postgresql or mysql; they don't use a temporary
table for table alterations.
Oh good :)
Can you open up the sqlite database if you
still have it and see what the contents of the migrate_tmp
Ira,
There is a known issue with resolving tool dependencies when running
functional tests. One workaround is to set the
GALAXY_TOOL_DEPENDENCY_DIR environment variable to the path configured
in your universe_wsgi.ini.
This issue is documented in https://trello.com/c/eVT3QWJF
--Dave B.
Peter,
I have duplicated this discrepancy in my local environment, and will be
looking into the cause. I hope to have it resolved in short order.
--Dave B.
On 5/9/13 06:06:16.000, Peter Cock wrote:
On Thu, May 9, 2013 at 10:59 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, May
On Thu, May 9, 2013 at 12:23 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hello all,
I'm exploring a conditional example where I would like to group some
of the select values into a single when clause. Currently it seems
each value requires its own when which leads to duplication and
This only affects tests that are run manually, the automated testing
framework correctly resolves tool dependencies.
--Dave B.
On 5/9/13 10:41:22.000, Peter Cock wrote:
On 5/8/13 20:08:08.000, Ira Cooke wrote:
Hi All,
I'm starting to add functional tests to my tools but I've found that
Hi Ramon,
I've committed a patch to the stable branch that should resolve this issue.
Please update your Galaxy instance and let us know if this has fixed it for you.
Thanks for using Galaxy,
Dan
On May 9, 2013, at 8:40 AM, Ramon Tiburski wrote:
Hi,
I uploaded some data and when I
Hi all,
For defining the 'install script' for some of my tool wrappers, I have
mainly following http://wiki.galaxyproject.org/ToolShedToolFeatures
and looking at one or two examples.
I've got some of my tools to work, but not all. For instance, this one
appears not to be downloading or moving
Hi Peter,
Hi all,
For defining the 'install script' for some of my tool wrappers, I have
mainly following http://wiki.galaxyproject.org/ToolShedToolFeatures
and looking at one or two examples.
I've got some of my tools to work, but not all. For instance, this one
appears not to be
On Thu, May 9, 2013 at 4:57 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Hi Peter,
Afaik download_by_url is only supported as first action. To work
around that limitation, until its fixed, I used wget to fetch any
additional file.
Ciao,
Björn
Interesting tip - I
Hi all,
There is probably a good reason for this, but why is Galaxy hiding
revisions from me on the main 'manage repository' page?
e.g. http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod
Here the drop down box only lets me view:
4:07f2d99bc2de (current tip)
0:f886a0b8b117
Why is it hiding
OK. thank you so much, but how can I update my instance?
Subject: Re: [galaxy-dev] UnicodeDecodeError: 'utf8' codec can't decode byte
0xb9 in position 15: invalid start byte
From: d...@bx.psu.edu
Date: Thu, 9 May 2013 11:02:46 -0400
CC: galaxy-dev@lists.bx.psu.edu
To:
Assuming you checked Galaxy out using mercurial, stop your Galaxy instance and
go into the Galaxy root directory and execute:
hg pull -u
Then start your Galaxy instance back up.
On May 9, 2013, at 12:36 PM, Ramon Tiburski wrote:
OK. thank you so much, but how can I update my instance?
Thank you so much
Subject: Re: [galaxy-dev] UnicodeDecodeError: 'utf8' codec can't decode byte
0xb9 in position 15: invalid start byte
From: d...@bx.psu.edu
Date: Thu, 9 May 2013 12:45:25 -0400
CC: galaxy-dev@lists.bx.psu.edu
To: ramao_tiago_tibur...@hotmail.com
Assuming you checked Galaxy out
Currently I feel that a tool dependency definition should allow for only a
singe download of some item, and if that item requires other items. they should
be defined as separate dependencies that are installed using the
prior_installation_required=True attribute.
Is there a case where this is
Only revisions that are associated with metadata are displayed in the select
list on the manage repository page because metadata is required to fill in the
contents of the page.
Metadata is generated for the following items currently - this list evolves
over time:
custom datatypes
valid/
Ah, forgot one:
tool functional test results
On May 9, 2013, at 1:11 PM, Greg Von Kuster wrote:
Only revisions that are associated with metadata are displayed in the select
list on the manage repository page because metadata is required to fill in
the contents of the page.
Metadata is
Hi Greg and Peter,
two examples from my side.
One of my tools (osra) has 7 dependencies. A few of them, GraphicsMagick
for example, makes sense to include as separate repo. But I feel that
the other are too special.
- openbabel (is an extra repo)
- GraphicsMagick
- potrace
- gocr
- tclap
-
Greg,
Thanks for the tip on Safari. I have switched to another browser and
working now!
Thanks,
-Adam
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information Technology
On Thu, May 9, 2013 at 6:05 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Currently I feel that a tool dependency definition should allow for only a
singe
download of some item, and if that item requires other items. they should be
defined as separate dependencies that are installed using the
On Thu, May 9, 2013 at 6:21 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Hi Greg and Peter,
two examples from my side.
One of my tools (osra) has 7 dependencies. A few of them, GraphicsMagick
for example, makes sense to include as separate repo. But I feel that
the
Peter,
As of my latest commit, the automated test results should now match that
of run_functional_tests.sh.
--Dave B.
On 5/9/13 06:06:16.000, Peter Cock wrote:
On Thu, May 9, 2013 at 10:59 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, May 9, 2013 at 10:49 AM, Peter Cock
Thanks for the reply..
Yeah i am using the Host=0.0.0.0 but i couldn't connect..
now after installing ngnix and reloading i am getting error like..
Traceback (most recent call last):
File ./scripts/paster.py, line 33, in module
serve.run()
File
Hello, Galaxy developers:
I'm a Galaxy user and to customize and deploy Galaxy server locally. I
need to build a connection between Galaxy and database server now. MySQL
and PostgreSQL are both configured to test the connection.
#for mysql server
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