Hi all,
I'd like to echo Florent's concern that run_functional_tests.sh
is too slow, and that this discourages Tool Authors from
adding more tests to their tools:
https://trello.com/c/wL21d2do/1017-functional-tests-take-too-long
(And encourage people to vote up that issue ;) )
Florent has ident
Peter,
Yes, the functional test suite is a bit on the slow side, and one of my
long-term goals has been to improve the performance as best I can.
--Dave B.
On 09/16/2013 07:24 AM, Peter Cock wrote:
Hi all,
I'd like to echo Florent's concern that run_functional_tests.sh
is too slow, and t
On Mon, Sep 16, 2013 at 2:30 PM, Dave Bouvier wrote:
> Peter,
>
> Yes, the functional test suite is a bit on the slow side, and one of my
> long-term goals has been to improve the performance as best I can.
>
Great - I appreciate there are lots of other high priority issues
with the test framewor
--Dave B.
On 09/16/2013 09:38 AM, Peter Cock wrote:
Separately, running the tests themselves seems overly
slow - can anything be tweaked here? For example, is
there any point executing the external set_meta script
in the test environment?
The switch to the external set_meta script was don
On Mon, Sep 16, 2013 at 2:56 PM, Dave Bouvier wrote:
> On 09/16/2013 09:38 AM, Peter Cock wrote:
>>
>> What I meant was, do we even need the metadata
>> for validating the test results? If not, skip generating it.
>
> Unfortunately, the metadata needs to be set in order
> to populate and validate
Hi,
I have developed a thin front end client in PHP to enable CILogon
authentication for Galaxy, and set up a dummy Galaxy instance demo at
https://gw64.iu.xsede.org. Please let me know if this is of interest to anyone
and I'd be happy share more details as well as the source. The choice of PHP
Hi,
I got this error when trying to install a repository I created
defining a tool dependency. The odd thing is the exact same definition
worked for the previous version of the same tool.
This is the repository failing to install, see full trace below:
http://testtoolshed.g2.bx.psu.edu/view/cjav/
Carlos,
The issue you're experiencing is due to features being added in the test
tool shed that have not yet been accounted for in Galaxy's stable
release to galaxy-dist. To resolve this issue, you'll need to be running
a recently updated checkout of galaxy-central on the default branch,
sinc
On Mon, Sep 16, 2013 at 8:57 PM, Carlos Borroto
wrote:
> I did an extra test. Started with a clean 'galaxy-dist'. This time
> both repositories fail with the same error. I guess before something
> was cached for the repository with version 0.1.4.
>
> I used biopython repository as a guide to write
On Mon, Sep 16, 2013 at 4:46 PM, Björn Grüning
wrote:
>>
>> Hi Peter,
>>
>> When I install my repository which has package_biopython_1_61 as a
>> dependency, package_atlas_3_10 and package_lapack_3_4 show as
>> "Installed, missing tool dependencies"(Grey). However
>> package_biopython_1_61 shows
You can overwrite your copy of the Cuffdiff wrapper at
tools/ngs_rna/cuffdiff_wrapper.xml with the new version:
https://bitbucket.org/galaxy/galaxy-central/raw/48fad71361b3075c85c7d365dd52c106cabad73a/tools/ngs_rna/cuffdiff_wrapper.xml
Best,
J.
On Sep 16, 2013, at 5:36 PM, Matthew Paul wrote:
I am not using CloudMan, but we do use a sqlite database. It seems to have
that behavior when there is an output that connects to two inputs... but I
think I need to do more investigating. I suppose we could try postgres and
see if that works...
- Nik.
On Mon, Sep 16, 2013 at 2:04 PM, Björn Gr
Over next couple days, I'll take a look at what's in
lib/galaxy/web/base/pluginframework.py and see if there is a way to refactor it
with my stuff in order to get a general plugin framework
(galaxy.pluginframework) as proposed by James. Sorry for the delay. Teaching a
math class this semester i
> hi Jeremy,
> in the histories controller, I could find no example to nicely obtain the PUT
> and POST content payload. Am I missing it?
> So I think a bad answer to my question is the following code. But I really
> don't like my _get_payload() hack reaching into the trans.environ object.
I wrote a very short update here:
http://galaxy-gsoc2013.blogspot.in/2013/09/penultimate-update.html
Saket
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and other Gala
Dear Galaxy hackers,
I'm having trouble with the tool test framework. I have a local
installation of a Galaxy Tool Shed (latest stable from the repository)
on my Linux server. I have an Apache proxy to my tool shed (per
http://wiki.galaxyproject.org/HostingALocalToolShed). The Tool Shed
seems to w
Hi all,
So we use Galaxy to teach our bioinformatics courses and we have an install
of Galaxy in the Amazon cloud that we have customized with various tools.
However, we don't touch the Galaxy code base itself. Recently, we've been
getting errors in creating and running workflows. We are getting
Hi,
I'm interested on running workflows with tool definitions containing
repeat inputs and arguments. I was wondering if there is a way to not
have to set a fix number of elements ahead of time in the workflow.
Thanks,
Carlos
___
Please keep
Serrano,
The GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF environment variable should be
set to an XML file that specifies the tool shed you're installing from.
I've updated the wiki page to be clearer on that point.
--Dave B.
On 09/16/2013 12:32 PM, Serrano Pereira wrote:
Dear Galaxy hackers,
I
Dave,
Thanks for your reply. I already had my tool shed specified in
tool_sheds_conf.xml, which is why I omitted the
GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF environment variable. I just tried
it with,
GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF=install_and_test_tool_sheds_conf.xml
The contents of the instal
It looks like you might have a space in your tool_sheds_conf.xml after
domain.org/ but before the " character, is that the case? If so, I would
suggest removing it and trying again.
--Dave B.
On 09/16/2013 03:26 PM, Serrano Pereira wrote:
Dave,
Thanks for your reply. I already had my tool
Thanks!. I was actually in the process of testing this combination. I
can confirm this error goes away when using a local instance of
galaxy-central instead.
On Mon, Sep 16, 2013 at 4:18 PM, Dave Bouvier wrote:
> Carlos,
>
> The issue you're experiencing is due to features being added in the test
On Mon, Sep 16, 2013 at 4:19 PM, Peter Cock wrote:
> On Mon, Sep 16, 2013 at 8:57 PM, Carlos Borroto
> wrote:
>> I did an extra test. Started with a clean 'galaxy-dist'. This time
>> both repositories fail with the same error. I guess before something
>> was cached for the repository with version
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