Re: [galaxy-dev] Installation of 20130603 Galaxy image with MySQL fails

11 Jun 2013

      Thanks Dannon.
I am going with postgres for now while mysql is being fixed.

Regards,
Linda

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.

  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