Hi Jeremy,
OK, that makes sense. Thanks again!
Clare
On 24 August 2012 02:17, Jeremy Goecks wrote:
>> I think that handle_input() executes the tool?
>
> That's the intention and it should work but it hasn't been tested.
>
>> Also, separately there
>> is a method called _run_tool() (although un
Hi guys,
I made a very small code change so that the workflows API will display
all the steps in a workflow, not just the inputs (these are still
displayed separately, as before). I made a pull request even though
the change is small, just to learn what I'm doing:
https://bitbucket.org/galaxy/gal
Hi John,
Thank you, this is really useful!
I don't understand the purpose of renaming the repository to
galaxy-central-new-feature - what does this achieve?
I'm pretty new to mercurial and more familiar with git, so that could
be why I'm confused.
Thanks,
Clare
On 24 August 2012 00:07, John Chi
We have a wiki page describing the addition of both simple and complex
datatypes, here's the link:
http://wiki.g2.bx.psu.edu/Admin/Datatypes/Adding%20Datatypes
Let me know if this isn't sufficient, and I can try to help.
-Dannon
On Aug 28, 2012, at 3:56 PM, Alfredo Guilherme Silva Souza
wrot
Good Afternoon.
I need to create a new data type in the galaxy, because I need to import a
file in the format. Pdb.
Someone already had to create a new kind of data?
Can you help?
Thank you.
--
*Alfredo Guilherme*
*
*
___
Please keep al
Hello Hans,
I've committed a fix for this issue in changeset 7560:738b703f725c, which will
be included in the next Galaxy release. Thanks for reporting this!
Greg Von Kuster
On Aug 28, 2012, at 5:40 AM, Hans-Rudolf Hotz wrote:
> Hi Greg
>
> Thank you for your help. Although, "integrated_tool
Dear Galaxy,
Last night (1AM) and today (10:45AM) I have not been able to return results
with the operate on genomic intervals, intersect tool. For example if I
upload ChIP-seq peak replicates in .gz format (downloaded directly from
ENCODE), no results are returned when they are intersected with
Dear Colleagues,
Many teams use module, a user interface for the Modules package. The
Modules package enable to manage easily several versions of a program with
a dynamic modification of the user's environment via modulefiles.
I would like to know if it is planned to integrate the ability to load
Hi Dan,
The only thing I can think of that is causing this behavior is an apache
rewrite rule that is not correctly handling your base URL. That's the only
scenario in which I've seen something like this occur, but others in the
community may have seen other causes. I'm fairly certain it has
On a related note, it's definitely nice to be able to consolidate the
configuration into a single universe_wsi.ini, but --daemon and --stop-daemon
are not sufficient for smooth operation of a multi web and job runner instance
of Galaxy. I wonder if anyone's already adapted run.sh to restart the
I've added this new feature in changeset 7556:c87370c5340d, which will be
available in the tool shed the next time it is updated. I'm making every
attempt to have the tool shed code base track the Galaxy distribution releases,
so the tool shed will probably not be updated until the next release
On Tue, Aug 28, 2012 at 2:30 PM, Greg Von Kuster wrote:
> HI Peter,
>
> On Aug 23, 2012, at 9:52 AM, Peter Cock wrote:
>
>> Hi Greg,
>>
>> Could you include .txt on the list of README
>> filenames looked for by the ToolShed as you said please?
>>
>> I've just checked and it isn't working at the mo
Philip,
Is it possible for you to upgrade your Galaxy instance code base to at least
changeset 2531e085f262 (the human-readable changeset revision is 7503)? I'm
not sure what is causing the behavior in your environment, but I had to upgrade
the tool shed to this rev in order to deal with some
On Aug 27, 2012, at 18:13, "Sebastian Schaaf"
wrote:
> If you refer to using one machine as master AND host simultaneously, which
> you never tried: let me tell you it does work well with SGE/OGE. I have it
> running, and it just works out great. It enhances the load control on that
> machine,
Hi Greg
Thank you for your help. Although, "integrated_tool_panel.xml" is
re-rewritten after each re-start, I can fix my problem (as you have
suggested) by removing it first, and then do a restart.
Regards,
Hans
On 08/27/2012 04:54 PM, Greg Von Kuster wrote:
Hi Hans,
Sorry, I missed your i
Thanks for the reply but no, I wasn't using any filters.
The relevant XML sections are like this:
...
Mutlu
On 24 August 2012 17:28, John Chilton wrote:
> I cannot speak to the code running twi, but are using a unique_value
> filter? The dynamic_options code use to completely lo
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