Please send your questions to the galaxy mailing lists ( galaxy-bugs(a)bx.psu.ed, galaxy-dev(a)bx.psu.edu, galaxy-user(a)bx.psu.edu ) instead of private email addresses as you will be much more likely to get answers in a timely fashion.
Given the context of your question, I assume you want to point another UCSC-like "get data" tool to your mirror. If that is the case, simply copy the ~/tools/data_source/ucsc_tablebrowser.xml file to a different file name (e.g., my_mirror.xml) , and edit the following line in it to point to your mirror:
<inputs action="http://genome.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get">
Next, add an entry for it in your tool_conf.xml file and restart your Galaxy instance.
That's all you should need.
On Mar 23, 2010, at 10:22 AM, Emeric Dubois wrote:
> Hello Greg
> I have installed a partial mirror of UCSC and Galaxy on my server.
> I want use my UCSC mirror to get data and display in my gallaxy installation.
> Is it possible to do that ? How ?
> Please, can you help me ?
> Emeric Dubois
> Plateforme MGX
> Institut de Génomique Fonctionnelle
> UMR 5203 CNRS – U 661 INSERM – Universite de Montpellier
> 141 rue de la cardonille
> 34094 Montpellier Cedex 05, France
> Tel: 04 67 14 29 32
> Ce message a été vérifié par MailScanner
> pour des virus ou des polluriels et rien de
> suspect n'a été trouvé.
Greg Von Kuster
Galaxy Development Team
I know that I have had the data transfer functionality working in the
past but it's currently failing ending with the following:
127.0.0.1 - - [23/Mar/2010:08:37:50 -0400] "GET
/user/create?username=nsfox1%40example.org&confirm=testuser&messagetype=error&msg=User+with+that+email+already+exists&password=testuser&email=nsfox1%40example.org HTTP/1.1" 200 - "-"
ERROR:root:Traceback (most recent call last):
File "scripts/galaxy_messaging/server/data_transfer.py", line 166,
raise DataTransferException("The "+self.datatx_email+" user could
not login to Galaxy")
DataTransferException: 'The nsfox1(a)example.org user could not login to Galaxy'
ERROR:root:FATAL ERROR.The nsfox1(a)example.org user could not login to Galaxy
DEBUG:root:[[u'data/ATC_AA', u'Error'], [u'data/ATC_AB', u'Error'],
[u'data/CRA_AC', u'Error'], [u'data/CRA_AE', u'In progress']]
[u'data/CRA_AE', u'Error.The nsfox1(a)example.org user could not login
I re-downloaded the Galaxy instance again but I'm still having this
issue. The user I'm using here is an admin user with permission to add
to the data library and when I go and login galaxy it works.
Any suggestions as to what I might be wrong would be great.
A small feature requested by our users:
The ability to set the axis ranges in the plotting tool (xy_plot.xml).
The attached patch adds this ability as an optional parameter in the tool.
Note1: if the input data goes beyond the user's suggest range, the range is extended.
Note2: the patch contains CR/LF because it appears the 'xy_plot.xml' tool has windows-style newlines.
I'm getting an error "AttributeError: 'StateColumn' object has no
attribute 'get_filter'" if I search anything on the sequencing request
page. Searching specifically within the Name search or Description
search does work though. Is this a known bug or did I possibly miss
setting up something in my Galaxy Instance?
Also, that search, which is currently not working for me, it only
searches the information the sequencing requests page, right? I'd like
to request being able to search the requests for something within the
request or have some where of quickly determining the information of
the sample with the requests without browsing to each one.
Any information is appreciated.