> I made some more modifications to the wrappers to allow for the tools to pull
> the genome information from the input files. The only drawback is that there
> is no way to validate whether the input has the dbkey attribute as a
> parameter (can you suggest a way to validate?). Attached are the
I get the following error from routes
AttributeError: 'thread._local' object has no attribute 'mapper'
-Original Message-
From: James Taylor [mailto:ja...@jamestaylor.org]
Sent: Thursday, October 20, 2011 5:46 PM
To: Chorny, Ilya
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev]
Excerpts from Chorny, Ilya's message of 2011-10-20 15:52:03 +:
> I thought I would add this to the list in case anyone in the galaxy :)
> knew the answer. I get a mapping error every time I invoke url_for.
> What variable stores the base url for the galaxy instance?
Can you provide the specif
Luciano,
You only need to create the database instance itself, you do not need to
manually create any tables. When you have created the database instance,
configure the path to it using the database_connection setting in
universe_wsgi.ini, something like:
database_connection = postgres:///gal
Hi,
I am sorry about the trivial questions. I am following this guide
http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP to set up a ftp
server to upload data to my local instance of galaxy. I am getting a error
when I am configuring the database server:
postgres@aedes:~$ createuser -SDR
Hi everybody,
we're hosting our own galaxy instance and the next step should bei the
integration of GeneTrack. (Not the tool, that is already included, but
the browser, which has to be set up on our own, as i could read on the
mailing list.)
I've been reading all information on http://genetr
Shaun,
we took this quite easily by a simple tool we added to the toolbox. Just use
the xml below as a new tool and you can get file paths of any file you like.
Hope it helps,
Alex
echo $input > $output
**What it does**
This tool gives the name of the data file from
SHAUN WEBB wrote:
>
> Hi Nate.
>
> Could you provide more info on how to run this script. I have a
> history and dataset name and I want to find the file stored on the
> server.
Hi Shaun,
You'll need the dataset ID, which you can see as part of the URL of many
of the links in the history item.
I am trying to display dataset paths in the UI when user clicks on the 'view
details' icon in the history panel. I was able to display it by adding
'hda.file_name' field in the show_params.mako template file and it seems to be
working. Following is a diff for it:
{{{
diff --git a/templates/sh
Hi Dan,
That's embarrassing - turns out I was editing the wrong XML file! That explains
it.
(I was working on it remotely, and I guess I didn't notice that I had lost the
connection - my text editor only saved my changes locally)
Thanks again for your help,
Alex
On Oct 20, 2011, at 9:33 AM, Dan
I thought I would add this to the list in case anyone in the galaxy :) knew the
answer. I get a mapping error every time I invoke url_for. What variable
stores the base url for the galaxy instance?
Thanks,
Ilya
-Original Message-
From: Chorny, Ilya
Sent: Wednesday, October 19, 2011 4
Hi Nate.
Could you provide more info on how to run this script. I have a
history and dataset name and I want to find the file stored on the
server.
Thanks
Shaun
Thanks Assaf,
This has come up enough times that I've just committed a script that
will return the filename if provided a nu
Hi Jeremy,
I made some more modifications to the wrappers to allow for the tools to pull
the genome information from the input files. The only drawback is that there is
no way to validate whether the input has the dbkey attribute as a parameter
(can you suggest a way to validate?). Attached are
Hi Alex,
The xml file you have attached has the "input_intervals" parameter set to
accept only gatk_intervals. If I swap it for the parameter that you listed
below (), then it works just fine and
will list bed files. Can you verify that the copy of the xml that you are
loading for the tool tha
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