An idea for sharing tools
by James Casbon
Hi Everyone,
I have an "I want a pony" idea that I would like to kick onto the mailing list:
It would be great if there was a way for sharing tool definitions between users.
At the moment, the main repo is maintained by the galaxy team, and
that is fine and makes sense. However, I'm sure there is a lot of
duplicated work between the users when adding other tools in. For
example, there was a conversation the other day about adding in awk.
Someone had already done this, so the best idea would be if I could
pull in that definition and enable it with minimum effort. I have
already added tools (exonerate, restriction mapper, etc, etc) that may
be of use to other people. Not sure the best way to go about this,
but if my understanding of mercurial is right, we can simply offer
another repo for people to pull changes from.
If this is of interest to you, please can you reply? If we get enough
interest and preferably some support of the core team, I could set up
a free repo at, e.g., bitbucket and add users to it. Or perhaps there
is a better way (eg patches submitted to trac)? Another question is
what kind of tools would the core team accept for inclusion in the
main dist?
Cheers,
James
13 years, 8 months
Exception when using remote_user.
by MORITA Hideyuki
Hi,
The following error will occur under certain condition when using remote_user.
AttributeError: 'NoneType' object has no attribute 'user'
This error is thrown when:
1. using remote_user
2. browser has a valid session (cookie)
3. after logged in with an email address other than previously used
This is caused by None value in prev_galaxy_session variable at L.231 in
lib/galaxy/web/framework/__init__.py.
I understand that galaxy_session instead of prev_galaxy_session should be
referenced here.
I created a patch to fix this problem by replacing prev_galaxy_session with
galaxy_session.
===================================================================================
diff -r a4214de3752e lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py Tue Feb 03 18:34:27 2009 -0500
+++ b/lib/galaxy/web/framework/__init__.py Mon Feb 16 13:31:02 2009 +0900
@@ -228,7 +228,7 @@ class UniverseWebTransaction( base.Defau
invalidate_existing_session = True
user_for_new_session = self.__get_or_create_remote_user( remote_user_email )
log.warning( "User logged in as '%s' externally, but has a cookie as '%s' invalidating session",
- remote_user_email, prev_galaxy_session.user.email )
+ remote_user_email, galaxy_session.user.email )
else:
# No session exists, get/create user for new session
user_for_new_session = self.__get_or_create_remote_user( remote_user_email )
===================================================================================
Thanks.
MORITA Hideyuki
13 years, 8 months
building python eggsfor Galaxy with python-2.6
by Amit Kr.. Mandal
Hello all,
I'm interested in adding tools and some long drawn jobs and hence trying to locally install Galaxy. My system is an Ubuntu 9.04 [Linux 2.6.28-11-generic; i686] with python 2.6.2.
As such I have to build the eggs using "scramble.py". All the eggs successfully build except the 'GeneTrack' egg (http://genetrack.googlecode.com/files/GeneTrack-1.0.3.zip).
The console output says -
scramble(): Beginning build
Traceback (most recent call last):
File "scramble.py", line 39, in <module>
execfile( "setup.py", globals(), locals() )
IOError: [Errno 2] No such file or directory: 'setup.py'
scramble(): Egg build failed for GeneTrack-1.0.3
I've attached a txt file with the detailed console output. Is the version of GeneTrack being downloaded wrong as per the Galaxy distribution (I've used mercurial to get the latest). Kindly help.
This would be too much to ask, but if anyone has compiled the egg on the same configuration, please share. It would be of great help!
thanks and regards,
Amit Kumar Mandal
Graduate Student
Genomics & Molecular Medicine
IGIB, Delhi
13 years, 8 months
Using postgresql instead of sqlite
by Akash Mohan
Hi All
In one of the pages you have mentioned that Galxy site on production server uses PostgreSql as the database. I tried searching for a guide to integrate postgresql to galaxy but could find one. Could you please provide me the steps to do so.
Thanks
Akash
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13 years, 8 months
