Hello,
I'm very new to Galaxy development. What we've got is a tool we've created
that will use our own API/web services in order to use BAM files in our
database as the data source in Galaxy.
I got it to work on a very tiny BAM file, but now that that is working, I tried
it on a larger one a
Dear all,
I'm still stuck with the problem to dynamically generate an option list
extracted from a user-selectable input dataset. Does anybody have
experience here, or is this not possible at all?
Have a nice weekend,
Holger
On 02/07/2012 09:58 PM, Holger Klein wrote:
> Dear all,
>
> I have a
I'll give it a try and let you know if I run into any more problemsThanksThonOn Feb 10, 2012, at 12:00 PM, Greg Von Kuster wrote:Thon, I believe this is fixed in change set 6711:62fc9e053835, which is now available in out central repo. However, I do not have access to any data of the required typ
Thon,
I believe this is fixed in change set 6711:62fc9e053835, which is now available
in out central repo. However, I do not have access to any data of the required
type, so if you still encounter problems, could you send me some data that I
can use to reproduce the behavior?
Thanks!
Greg
O
What revision is your Galaxy instance at? I'm not seeing this behavior on tip
with a simple test, it may have been something we've fixed in a more recent
revision.
-Dannon
On Feb 10, 2012, at 11:14 AM, Petit III, Robert A. wrote:
> Hi there,
>
> I've run into an issue on my local galaxy inst
>
> Wouldn't it be better not to have the default value 40 (or 20) in the wrapper
> at all? i.e. Leave it out, so that by default that argument isn't used, so
> that
> tophat uses the default it wants to use.
This would work but limits reproducibility and transparency because Galaxy
wouldn't ha
On Fri, Feb 10, 2012 at 4:18 PM, Jeremy Goecks wrote:
>> On Thu, Feb 9, 2012 at 11:27 PM, Andrew Warren wrote:
>>> Hello,
>>>
>>> I was recently adjusting advanced parameters when running Tophat in Galaxy
>>> and noticed that when advanced parameters are used, every field is converted
>>> and sub
> On Thu, Feb 9, 2012 at 11:27 PM, Andrew Warren wrote:
>> Hello,
>>
>> I was recently adjusting advanced parameters when running Tophat in Galaxy
>> and noticed that when advanced parameters are used, every field is converted
>> and submitted as command line parameter to the tool at runtime. Wit
Hi there,
I've run into an issue on my local galaxy install. When I have 20 or more
datasets in my history, I no longer get the option to 'Enable/Disable selection
of multiple input files...' I instead get a broken drop down list. I say
broken because its as though the drop down list and input
Hi all,
I've just updated our Galaxy to the current release 26920e20157f which
now includes quota support. This means I need to run
set_dataset_sizes.py in order to record the current usage, as
explained here:
http://wiki.g2.bx.psu.edu/Admin/Disk%20Quotas
However, I have run into a problem:
$ su
Hello all,
I've noticed we have about a dozen stalled upload jobs on our server
from several users. e.g.
Job ID UserLast Update ToolState Command LineJob Runner
PID/Cluster ID
235221 hours agoupload1 upload NoneNoneNone
...
2339
On Thu, Feb 9, 2012 at 11:27 PM, Andrew Warren wrote:
> Hello,
>
> I was recently adjusting advanced parameters when running Tophat in Galaxy
> and noticed that when advanced parameters are used, every field is converted
> and submitted as command line parameter to the tool at runtime. Without
> c
On Thu, Feb 9, 2012 at 9:57 PM, Jennifer Jackson wrote:
> Hi Peter,
>
> It looks to me like there are versions both, with the Tool Shed version
> having the more recent date stamp. But if those extra functions are not
> needed, then yes, you are correct, the version included in the distribution
>
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