Thanks Dannon.
I am going with postgres for now while mysql is being fixed.
Regards,
Linda
Dannon Baker ---06/06/2013 04:41:53 PM---Hi Linda, Sorry I wasn't clear before. The fix for that first issue is in
From: Dannon Baker <dannon.baker@gmail.com>
To: Linda Cham/Poughkeepsie/IBM@IBMUS
Cc: Björn Grüning <bjoern.gruening@pharmazie.uni-freiburg.de>, Galaxy Dev <galaxy-dev@lists.bx.psu.edu>
Date: 06/06/2013 04:41 PM
Subject: Re: [galaxy-dev] Installation of 20130603 Galaxy image with MySQL fails
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.
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