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

2013-06-21 Thread jean-François Taly 

Dear all,

I am having the same problem as Linda with a fresh installation of 
version 20130603.

In the thread of her mail Dannon Baker said :
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.


I would like to know if what is the status of this thread. Should I use 
the solution provided in Linda's mail (CREATE INDEX ix_history_slug ON 
history (slug(1000));)


Thx a lot for your help

Best

Jean-François



On 06/05/2013 05:12 PM, Linda Cham wrote:
Hi.   I am new to the Galaxy forum and I am trying to setup a new 
local Galaxy instance with MySQL on RH6.2 x86_64.


On a newly installed OS node, using the hg clone command (hg clone 
_https://bitbucket.org/galaxy/galaxy-dist#stable_ 
https://bitbucket.org/galaxy/galaxy-dist) which gets the current 
Galaxy 20130603 image, I am getting the following errors when running 
run.sh:
  File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py, line 
173, in execute

self.errorhandler(self, exc, value)
  File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py, 
line 36, in defaulterrorhandler

raise errorclass, errorvalue
OperationalError: (OperationalError) (1170, BLOB/TEXT column 'slug' 
used in key specification without a key length) 'CREATE INDEX 
ix_history_slug ON history (slug)' ()


Reading the forum, someone stated it can be bypass by running the 
CREATE INDEX.


mysql CREATE INDEX ix_history_slug ON history (slug(1000));
Query OK, 0 rows affected (0.09 sec)
Records: 0  Duplicates: 0  Warnings: 0



--
#
Jean-François Taly
Bioinformatician

Bioinformatics Core Facility
http://biocore.crg.cat
CRG - Centre de Regulació Genòmica (Room 439)
Parc de Recerca Biomèdica de Barcelona (PRBB)
Doctor Aiguader, 88
08003 Barcelona
Spain

email: jean-francois.t...@crg.eu
phone: +34 93 316 0202
fax: +34 93 316 0099
#

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

2013-06-21 Thread Dannon Baker 
Hi Jean-François,

The index issues preventing a new instance from starting are resolved in
the stable branch of galaxy-central; if you pull updates from that branch
you should be able to start a new instance.  While the instance will start
and run, there are other peculiarities I still need to resolve and I'd
really recommend using postgres for a new instance at this time if you're
at all able to do so.

-Dannon


On Fri, Jun 21, 2013 at 5:07 AM, jean-François Taly 
jean-francois.t...@crg.eu wrote:

  Dear all,

 I am having the same problem as Linda with a fresh installation of version
 20130603.
 In the thread of her mail Dannon Baker said :

 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.

 I would like to know if what is the status of this thread. Should I use
 the solution provided in Linda's mail (CREATE INDEX ix_history_slug ON
 history (slug(1000));)

 Thx a lot for your help

 Best

 Jean-François




 On 06/05/2013 05:12 PM, Linda Cham wrote:

 Hi.   I am new to the Galaxy forum and I am trying to setup a new local
 Galaxy instance with MySQL on RH6.2 x86_64.

 On a newly installed OS node, using the hg clone command (hg clone *
 https://bitbucket.org/galaxy/galaxy-dist#stable*https://bitbucket.org/galaxy/galaxy-dist)
 which gets the current Galaxy 20130603 image, I am getting the following
 errors when running run.sh:
   File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py, line 173,
 in execute
 self.errorhandler(self, exc, value)
   File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py, line
 36, in defaulterrorhandler
 raise errorclass, errorvalue
 OperationalError: (OperationalError) (1170, BLOB/TEXT column 'slug' used
 in key specification without a key length) 'CREATE INDEX ix_history_slug
 ON history (slug)' ()

 Reading the forum, someone stated it can be bypass by running the CREATE
 INDEX.

 mysql CREATE INDEX ix_history_slug ON history (slug(1000));
 Query OK, 0 rows affected (0.09 sec)
 Records: 0  Duplicates: 0  Warnings: 0



 --
 #
 Jean-François Taly
 Bioinformatician

 Bioinformatics Core Facilityhttp://biocore.crg.cat
 CRG - Centre de Regulació Genòmica (Room 439)
 Parc de Recerca Biomèdica de Barcelona (PRBB)
 Doctor Aiguader, 88
 08003 Barcelona
 Spain

 email: jean-francois.t...@crg.eu
 phone: +34 93 316 0202
 fax: +34 93 316 0099
 #



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

2013-06-21 Thread jean-François Taly 

Thanks Dannon,

I indeed managed to have the galaxy-central version installed.
I already see some problems but I will open another thread if necessary.

Regards the DB engine, this new Galaxy I am deploying now is only a toy 
server I want to use in the Galaxy meeting in Oslo.
I would like to have the same configuration as the other server we 
already have which using MySQL.


Thx a lot for your help

JF



On 06/21/2013 11:26 AM, Dannon Baker wrote:

Hi Jean-François,

The index issues preventing a new instance from starting are resolved 
in the stable branch of galaxy-central; if you pull updates from that 
branch you should be able to start a new instance.  While the instance 
will start and run, there are other peculiarities I still need to 
resolve and I'd really recommend using postgres for a new instance at 
this time if you're at all able to do so.


-Dannon


On Fri, Jun 21, 2013 at 5:07 AM, jean-François Taly 
jean-francois.t...@crg.eu mailto:jean-francois.t...@crg.eu wrote:


Dear all,

I am having the same problem as Linda with a fresh installation of
version 20130603.
In the thread of her mail Dannon Baker said :

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.

I would like to know if what is the status of this thread. Should
I use the solution provided in Linda's mail (CREATE INDEX
ix_history_slug ON history (slug(1000));)

Thx a lot for your help

Best

Jean-François




On 06/05/2013 05:12 PM, Linda Cham wrote:

Hi.   I am new to the Galaxy forum and I am trying to setup a new
local Galaxy instance with MySQL on RH6.2 x86_64.

On a newly installed OS node, using the hg clone command (hg
clone _https://bitbucket.org/galaxy/galaxy-dist#stable_
https://bitbucket.org/galaxy/galaxy-dist) which gets the
current Galaxy 20130603 image, I am getting the following errors
when running run.sh:
  File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py,
line 173, in execute
self.errorhandler(self, exc, value)
  File
build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py, line
36, in defaulterrorhandler
raise errorclass, errorvalue
OperationalError: (OperationalError) (1170, BLOB/TEXT column
'slug' used in key specification without a key length) 'CREATE
INDEX ix_history_slug ON history (slug)' ()

Reading the forum, someone stated it can be bypass by running the
CREATE INDEX.

mysql CREATE INDEX ix_history_slug ON history (slug(1000));
Query OK, 0 rows affected (0.09 sec)
Records: 0  Duplicates: 0  Warnings: 0



-- 
#

Jean-François Taly
Bioinformatician

Bioinformatics Core Facility
http://biocore.crg.cat
CRG - Centre de Regulació Genòmica (Room 439)
Parc de Recerca Biomèdica de Barcelona (PRBB)
Doctor Aiguader, 88
08003 Barcelona
Spain

email:jean-francois.t...@crg.eu  mailto:jean-francois.t...@crg.eu
phone:+34 93 316 0202  tel:%2B34%2093%20316%200202
fax:+34 93 316 0099  tel:%2B34%2093%20316%200099
#


___
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--
#
Jean-François Taly
Bioinformatician

Bioinformatics Core Facility
http://biocore.crg.cat
CRG - Centre de Regulació Genòmica (Room 439)
Parc de Recerca Biomèdica de Barcelona (PRBB)
Doctor Aiguader, 88
08003 Barcelona
Spain

email:jean-francois.t...@crg.eu
phone: +34 93 316 0202
fax: +34 93 316 0099
#

___
Please keep all replies on the list by using reply all
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: [galaxy-dev] Installation of 20130603 Galaxy image with MySQL fails

2013-06-11 Thread Linda Cham 

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

Regards,
Linda




From:   Dannon Baker dannon.ba...@gmail.com
To: Linda Cham/Poughkeepsie/IBM@IBMUS
Cc: Björn Grüning bjoern.gruen...@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 lc...@us.ibm.com wrote:
  Hi Bjorn,

  Currently seen
  $ hg tip
  changeset:   9850:cea3ddf6cdda
  branch:      stable
  tag:         tip
  user:        Nate Coraor n...@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 n...@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 n...@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 n...@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.gruen...@pharmazie.uni-freiburg.de
  To: Linda Cham/Poughkeepsie/IBM@IBMUS
  Cc: Dannon Baker dannon.ba...@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






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

2013-06-06 Thread Dannon Baker 
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 lc...@us.ibm.com wrote:

 Hi Bjorn,

 Currently seen
 $ hg tip
 changeset:   9850:cea3ddf6cdda
 branch:  stable
 tag: tip
 user:Nate Coraor n...@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*https://bitbucket.org/galaxy/galaxy-dist
 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 n...@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 n...@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 n...@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.


 [image: 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.gruen...@pharmazie.uni-freiburg.de
 To: Linda Cham/Poughkeepsie/IBM@IBMUS
 Cc: Dannon Baker dannon.ba...@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



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

2013-06-05 Thread Dannon Baker 
Hi Linda,

The decorator issue should be resolved in galaxy-central now.  I'm setting
up a test environment to see if I can reproduce the mysql issue now, and
will let you know what I come up with.

Thanks!

-Dannon


On Wed, Jun 5, 2013 at 11:12 AM, Linda Cham lc...@us.ibm.com wrote:

 Hi.   I am new to the Galaxy forum and I am trying to setup a new local
 Galaxy instance with MySQL on RH6.2 x86_64.

 On a newly installed OS node, using the hg clone command (hg clone *
 https://bitbucket.org/galaxy/galaxy-dist#stable*https://bitbucket.org/galaxy/galaxy-dist)
 which gets the current Galaxy 20130603 image, I am getting the following
 errors when running run.sh:
   File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py, line 173,
 in execute
 self.errorhandler(self, exc, value)
   File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py, line
 36, in defaulterrorhandler
 raise errorclass, errorvalue
 OperationalError: (OperationalError) (1170, BLOB/TEXT column 'slug' used
 in key specification without a key length) 'CREATE INDEX ix_history_slug
 ON history (slug)' ()

 Reading the forum, someone stated it can be bypass by running the CREATE
 INDEX.

 mysql CREATE INDEX ix_history_slug ON history (slug(1000));
 Query OK, 0 rows affected (0.09 sec)
 Records: 0  Duplicates: 0  Warnings: 0

 When trying to run.sh again after the CREATE INDEX, will get this error:
   File /gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/lib/galaxy/app.py,
 line 52, in __init__
 create_or_verify_database( db_url, kwargs.get( 'global_conf', {}
 ).get( '__file__', None ), self.config.database_engine_options, app=self )
   File
 /gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/lib/galaxy/model/migrate/check.py,
 line 107, in create_or_verify_database
 % ( db_schema.version, migrate_repository.versions.latest, config_arg
 ) )
 Exception: Your database has version '29' but this code expects version
 '115'.  Please backup your database and then migrate the schema by running
 'sh manage_db.sh upgrade'.

 So try to run the sh manage_db.sh upgrade' now will get this error:
 $ sh manage_db.sh upgrade
 Traceback (most recent call last):
   File ./scripts/manage_db.py, line 13, in module
 from migrate.versioning.shell import main
   File
 /gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/shell.py,
 line 12, in module
 from migrate.versioning import api
   File
 /gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/api.py,
 line 33, in module
 from migrate.versioning import (repository, schema, version,
   File
 /gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/repository.py,
 line 13, in module
 from migrate.versioning import version, pathed, cfgparse
   File
 /gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/version.py,
 line 10, in module
 from migrate.versioning import pathed, script
   File
 /gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/pathed.py,
 line 11, in module
 from migrate.versioning.util import KeyedInstance
   File
 /gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/util/__init__.py,
 line 7, in module
 from decorator import decorator
 ImportError: No module named decorator

 In some searches, there were tips of deleting the eggs directory and rerun
 run.sh or use a python env.  Neither option worked.
 Was not able to find anything meaningful about the decorator error.

 Note:, I was able to get Galaxy up with MySQL using the Galaxy
 788cd3d06541 image on a different node.  So I am thinking maybe it is the
 new 20130603 image that is giving me issues?

 Commands used to get Galaxy up:

Install mysql from yum repository [MySQL 5.1.52-1.el6_0.1]
python version [2.6.6]

Grant ALL PRIVILEGES galaxy_db.* TO  galaxy_user on localhostname with
PWD
Images tested:

*Copy of the galaxy-galaxy-dist-788cd3d06541.tar.bz2 image  Did not
run the hg update command. [This worked]

*hg clone stable of newest image [Failed]

Update the universe_wsg.ini with the port, host, database_connection
to mysql

Ran run.sh



 Thanks.

 Linda


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

2013-06-05 Thread Linda Cham 

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:

  File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py, line 173, in
execute
  File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py, line 36,
in defaulterrorhandler
sqlalchemy.exc.OperationalError: (OperationalError) (1060, Duplicate
column name 'slug') '\nALTER TABLE history ADD slug TEXT' ()

So I thought maybe I should remove the column that was added before.

ALTER TABLE history DROP COLUMN slug;

Ran the sh manage_db.sh upgrade again, but now it gives back the original
error:

  File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py, line 36,
in defaulterrorhandler
sqlalchemy.exc.OperationalError: (OperationalError) (1170, BLOB/TEXT
column 'slug' used in key specification without a key length) 'CREATE
INDEX ix_history_slug ON history (slug)' ()

Interesting to note that if I ran the sh manage_db.sh again after the
CREATE INDEX error above, I get back this error now:
  File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py, line 36,
in defaulterrorhandler
sqlalchemy.exc.OperationalError: (OperationalError) (1060, Duplicate
column name 'slug') '\nALTER TABLE history ADD slug TEXT' ()






Hi Linda,

The decorator issue should be resolved in galaxy-central now.  I'm setting
up a test environment to see if I can reproduce the mysql issue now, and
will let you know what I come up with.

Thanks!

-Dannon


On Wed, Jun 5, 2013 at 11:12 AM, Linda Cham lc...@us.ibm.com wrote:
  Hi.   I am new to the Galaxy forum and I am trying to setup a new local
  Galaxy instance with MySQL on RH6.2 x86_64.

  On a newly installed OS node, using the hg clone command (hg clone
  https://bitbucket.org/galaxy/galaxy-dist#stable) which gets the current
  Galaxy 20130603 image, I am getting the following errors when running
  run.sh:
    File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py, line 173,
  in execute
      self.errorhandler(self, exc, value)
    File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py, line
  36, in defaulterrorhandler
      raise errorclass, errorvalue
  OperationalError: (OperationalError) (1170, BLOB/TEXT column 'slug' used
  in key specification without a key length) 'CREATE INDEX ix_history_slug
  ON history (slug)' ()

  Reading the forum, someone stated it can be bypass by running the CREATE
  INDEX.

  mysql CREATE INDEX ix_history_slug ON history (slug(1000));
  Query OK, 0 rows affected (0.09 sec)
  Records: 0  Duplicates: 0  Warnings: 0

  When trying to run.sh again after the CREATE INDEX, will get this error:
    File /gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/lib/galaxy/app.py,
  line 52, in __init__
      create_or_verify_database( db_url, kwargs.get( 'global_conf',
  {} ).get( '__file__', None ), self.config.database_engine_options,
  app=self )
    File
  
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/lib/galaxy/model/migrate/check.py,
 line 107, in create_or_verify_database
      % ( db_schema.version, migrate_repository.versions.latest,
  config_arg ) )
  Exception: Your database has version '29' but this code expects version
  '115'.  Please backup your database and then migrate the schema by
  running 'sh manage_db.sh upgrade'.

  So try to run the sh manage_db.sh upgrade' now will get this error:
  $ sh manage_db.sh upgrade
  Traceback (most recent call last):
    File ./scripts/manage_db.py, line 13, in module
      from migrate.versioning.shell import main
    File
  
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/shell.py,
 line 12, in module
      from migrate.versioning import api
    File
  
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/api.py,
 line 33, in module
      from migrate.versioning import (repository, schema, version,
    File
  
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/repository.py,
 line 13, in module
      from migrate.versioning import version, pathed, cfgparse
    File
  
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/version.py,
 line 10, in module
      from migrate.versioning import pathed, script
    File
  
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/pathed.py,
 line 11, in module
      from migrate.versioning.util import KeyedInstance
    File
  
/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/util/__init__.py,
 line 7, in module
      from decorator import decorator
  ImportError: No module named decorator

  In some searches, there were tips of deleting the eggs directory and
  rerun run.sh or use a python env.  Neither option

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

2013-06-05 Thread Björn Grüning 
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 

   File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py, line
 173, in execute
   File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py,
 line 36, in defaulterrorhandler
 sqlalchemy.exc.OperationalError: (OperationalError) (1060, Duplicate
 column name 'slug') '\nALTER TABLE history ADD slug TEXT' ()
 
 So I thought maybe I should remove the column that was added before.
 
 ALTER TABLE history DROP COLUMN slug;
 
 Ran the sh manage_db.sh upgrade again, but now it gives back the
 original error:
 
   File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py,
 line 36, in defaulterrorhandler
 sqlalchemy.exc.OperationalError: (OperationalError) (1170, BLOB/TEXT
 column 'slug' used in key specification without a key length) 'CREATE
 INDEX ix_history_slug ON history (slug)' ()
 
 Interesting to note that if I ran the sh manage_db.sh again after the
 CREATE INDEX error above, I get back this error now:
   File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py,
 line 36, in defaulterrorhandler
 sqlalchemy.exc.OperationalError: (OperationalError) (1060, Duplicate
 column name 'slug') '\nALTER TABLE history ADD slug TEXT' ()
 
 
 
 
 Inactive hide details for Dannon Baker ---06/05/2013 11:40:32 AM---Hi
 Linda, The decorator issue should be resolved in galaxy-cDannon Baker
 ---06/05/2013 11:40:32 AM---Hi Linda, The decorator issue should be
 resolved in galaxy-central now.  I'm setting
 
 Hi Linda,
 
 The decorator issue should be resolved in galaxy-central now.  I'm
 setting up a test environment to see if I can reproduce the mysql
 issue now, and will let you know what I come up with.
 
 Thanks!
 
 -Dannon
 
 
 On Wed, Jun 5, 2013 at 11:12 AM, Linda Cham lc...@us.ibm.com wrote: 
 
 Hi.   I am new to the Galaxy forum and I am trying to setup a
 new local Galaxy instance with MySQL on RH6.2 x86_64.
 
 On a newly installed OS node, using the hg clone command (hg
 clone https://bitbucket.org/galaxy/galaxy-dist#stable) which
 gets the current Galaxy 20130603 image, I am getting the
 following errors when running run.sh:
   File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py,
 line 173, in execute
 self.errorhandler(self, exc, value)
   File
 build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py,
 line 36, in defaulterrorhandler
 raise errorclass, errorvalue
 OperationalError: (OperationalError) (1170, BLOB/TEXT column
 'slug' used in key specification without a key length)
 'CREATE INDEX ix_history_slug ON history (slug)' ()
 
 Reading the forum, someone stated it can be bypass by running
 the CREATE INDEX.
 
 mysql CREATE INDEX ix_history_slug ON history (slug(1000));
 Query OK, 0 rows affected (0.09 sec)
 Records: 0  Duplicates: 0  Warnings: 0
 
 When trying to run.sh again after the CREATE INDEX, will get
 this error:
   File
 /gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/lib/galaxy/app.py, line 
 52, in __init__
 create_or_verify_database( db_url,
 kwargs.get( 'global_conf', {} ).get( '__file__', None ),
 self.config.database_engine_options, app=self )
   File
 
 /gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/lib/galaxy/model/migrate/check.py,
  line 107, in create_or_verify_database
 % ( db_schema.version, migrate_repository.versions.latest,
 config_arg ) )
 Exception: Your database has version '29' but this code
 expects version '115'.  Please backup your database and then
 migrate the schema by running 'sh manage_db.sh upgrade'.
 
 So try to run the sh manage_db.sh upgrade' now will get this
 error:
 $ sh manage_db.sh upgrade
 Traceback (most recent call last):
   File ./scripts/manage_db.py, line 13, in module
 from migrate.versioning.shell import main
   File
 
 /gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/shell.py,
  line 12, in module
 from migrate.versioning import api
   File
 
 /gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/api.py,
  line 33, in module
 from migrate.versioning import (repository, schema,
 version,
   File

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

2013-06-05 Thread Linda Cham 

Hi Bjorn,

Currently seen
$ hg tip
changeset:   9850:cea3ddf6cdda
branch:  stable
tag: tip
user:Nate Coraor n...@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 n...@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 n...@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 n...@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.




From:   Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de
To: Linda Cham/Poughkeepsie/IBM@IBMUS
Cc: Dannon Baker dannon.ba...@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

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