Hi Linda,

Sorry I wasn't clear before.  The fix for that first issue is in galaxy-central's stable branch, which will be migrated to galaxy-dist probably sometime next week.  You can always pull directly from -central though, using 'hg pull -u -b stable http://bitbucket.org/galaxy/galaxy-central/'

That said, this doesn't resolve the mysql index issues, which I'm currently working on.  I hope to have a fix for them available soon, though.

-Dannon


On Wed, Jun 5, 2013 at 4:47 PM, Linda Cham <lcham@us.ibm.com> wrote:

Hi Bjorn,

Currently seen
$ hg tip
changeset:   9850:cea3ddf6cdda
branch:      stable
tag:         tip
user:        Nate Coraor <nate@bx.psu.edu>
date:        Mon Jun 03 16:17:31 2013 -0400
summary:     Update tag for stable_2013.06.03

Removed galaxy-dist directory and rerun the hg clone command.

$ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable
destination directory: galaxy-dist
requesting all changes
adding changesets
adding manifests
adding file changes
added 9851 changesets with 36400 changes to 7175 files
updating to branch stable
4132 files updated, 0 files merged, 0 files removed, 0 files unresolved

$ cd galaxy-dist
$ hg heads
changeset:   9850:cea3ddf6cdda
branch:      stable
tag:         tip
user:        Nate Coraor <nate@bx.psu.edu>
date:        Mon Jun 03 16:17:31 2013 -0400
summary:     Update tag for stable_2013.06.03

$ hg pull ; hg update stable
pulling from https://bitbucket.org/galaxy/galaxy-dist
searching for changes
no changes found
0 files updated, 0 files merged, 0 files removed, 0 files unresolved

Check the script/manage_db.py:
from galaxy import eggs
                                                  <----- No decorator line
eggs.require( "Tempita" )
eggs.require( "SQLAlchemy" )
eggs.require( "sqlalchemy_migrate" )


$ hg update tip
0 files updated, 0 files merged, 0 files removed, 0 files unresolved

$ hg heads
changeset:   9850:cea3ddf6cdda
branch:      stable
tag:         tip
user:        Nate Coraor <nate@bx.psu.edu>
date:        Mon Jun 03 16:17:31 2013 -0400
summary:     Update tag for stable_2013.06.03

$ hg update default
82 files updated, 0 files merged, 2 files removed, 0 files unresolved

$ hg heads
changeset:   9850:cea3ddf6cdda
branch:      stable
tag:         tip
user:        Nate Coraor <nate@bx.psu.edu>
date:        Mon Jun 03 16:17:31 2013 -0400
summary:     Update tag for stable_2013.06.03

script/manage_db.py still the same as above.


Inactive hide details for Björn Grüning ---06/05/2013 04:30:09 PM---Hi Linda, > Hi Dannon,Björn Grüning ---06/05/2013 04:30:09 PM---Hi Linda, > Hi Dannon,

From: Björn Grüning <bjoern.gruening@pharmazie.uni-freiburg.de>
To: Linda Cham/Poughkeepsie/IBM@IBMUS
Cc: Dannon Baker <dannon.baker@gmail.com>, Galaxy Dev <galaxy-dev@lists.bx.psu.edu>
Date: 06/05/2013 04:30 PM
Subject: Re: [galaxy-dev] Installation of 20130603 Galaxy image with MySQL fails




Hi Linda,

> Hi Dannon,
>
> Thanks.  I tried to do the hg pull and update and hg tip but I do not
> see the changes in my working directory.  So I added the one liner
> eggs.require( "decorator" ) to scripts/manage_db.py.
> Ran the sh manage_db.sh upgrade and get this error:

that is really strange. Can you show us what the output of hg tip is?
Do you mind to start with a fresh checkout and that particular change?

Thanks,
Björn