On Thu, May 9, 2013 at 10:49 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
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
On Thu, May 9, 2013 at 6:59 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
As of my latest commit, the automated test results should now match that of
run_functional_tests.sh.
--Dave B.
Thanks Dave,
Presumably once the Test Tool Shed is updated, all the old tests will be re-run,
and so
Hello all,
I'm testing a workflow which uses my filter tool where one of the parameters
is a tabular file, and a related parameter is a multi-column selector:
Tool:
http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
Snippet from tool XML,
param name=input_tabular type=data
That is correct, the tests are run nightly, some time after midnight
eastern US time, unless I manually initiate the testing process.
--Dave B.
On 5/10/13 05:36:41.000, Peter Cock wrote:
On Thu, May 9, 2013 at 6:59 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
As of my latest commit,
Is there a more optimal time to initiate this testing process to better
accommodate those in other time zones? If anyone is waiting for the nightly
test results, we should tweak cron so no waiting is necessary (if possible).
On May 10, 2013, at 8:53 AM, Dave Bouvier wrote:
That is correct,
Buildbot can be triggered here
http://buildbot.g2.bx.psu.edu/builders/central-py2.7-linux-x86_64-postgres
manually
I think.
On Fri, May 10, 2013 at 10:56 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Is there a more optimal time to initiate this testing process to better
accommodate those in
On Fri, May 10, 2013 at 1:51 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
The automated testing framework consists of a series of scripts that run in
a certain order, so between one script and the next, there may sometimes be
unexpected results displayed. I've had a look at the repositories
On Thu, May 9, 2013 at 4:39 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
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
Hi Peter,
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
Hi Kathryn,
It looks like you haven't installed FastQC (or potentially installed it and
just haven't made it accessible to Galaxy). You'll need to install FastQC
from http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ if you
haven't already, and the main fastqc perl script must be
Hey Peter,
You're correct, currently the only top level description field for a
workflow is that Annotation/Notes field. While it wouldn't have rich text,
is it reasonable to programmatically generate something like what you're
suggesting from the combination of the primary Annotation/Notes
Björn, Peter,
I've created a trello card (https://trello.com/c/QY0Z7L7p) for this
requirement, and will be working on enhancing that feature as my next
priority.
--Dave B.
On 5/10/13 09:59:37.000, Björn Grüning wrote:
Hi Peter,
For defining the 'install script' for some of my tool
On Fri, May 10, 2013 at 3:10 PM, Dannon Baker dannon.ba...@gmail.com wrote:
Hey Peter,
You're correct, currently the only top level description field for a
workflow is that Annotation/Notes field. While it wouldn't have rich text,
is it reasonable to programmatically generate something like
On Fri, May 10, 2013 at 2:59 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Hi Peter,
I believe that either I have a simple error in both install descriptions,
leading to the install to 'work' but not put things where I expect them
(which is my problem), or the install is
Peter,
Yes, jar files are just a directory of .class (and other) files packaged
with the zip algorithm, which has its benefits and drawbacks, as you've
discovered. In the new action type I'm working on, I do intend to
include the option to extract a downloaded file, or leave it as-is,
which
Do you think we could add a new 'rich text' field for a workflow free
text help / readme file?
Annotations will support HTML, and it's always been the long-term plan that
they will include HTML. What's missing is a nice editor for creating HTML
annotations.
J.
On Fri, May 10, 2013 at 5:07 PM, Jeremy Goecks jeremy.goe...@emory.edu wrote:
Do you think we could add a new 'rich text' field for a workflow free
text help / readme file?
Annotations will support HTML, and it's always been the long-term
plan that they will include HTML. What's missing is a
Peter,
As of 9696:b4733e42a2c9, Galaxy now supports an additional tool
dependency installation action called download_file, which downloads a
file from the specified URL and saves it to the current working
directory, without extracting it. The format is:
action
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