Installation of 20130603 Galaxy image with MySQL fails
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 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
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 <lcham@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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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 <lcham@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 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 ___________________________________________________________ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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 <lcham@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 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
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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. 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
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*<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 <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.
[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.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
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
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.taly@crg.eu phone: +34 93 316 0202 fax: +34 93 316 0099 #####################################
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.taly@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.taly@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: http://lists.bx.psu.edu/
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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.taly@crg.eu <mailto:jean-francois.taly@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.taly@crg.eu <mailto:jean-francois.taly@crg.eu> phone:+34 93 316 0202 <tel:%2B34%2093%20316%200202> fax:+34 93 316 0099 <tel:%2B34%2093%20316%200099> #####################################
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- ##################################### 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.taly@crg.eu phone: +34 93 316 0202 fax: +34 93 316 0099 #####################################
participants (4)
-
Björn Grüning -
Dannon Baker -
jean-François Taly -
Linda Cham