Thanks Brad!  I updated with hg pull -u and then ran "sh manage_db.sh upgrade" but I have an error.  Could you help?  I backed up my database before I ran the upgrade script, so I can go back in time.

(sorry about the wall of text)

109 -> 110...
/home/galaxy/bin/chapman-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/dialects/sqlite/base.py:723: SAWarning: Did not recognize type 'BIGINT' of column 'bytes'

Add UUID column to dataset table

done
110 -> 111...

Add support for job destinations to the job table

done
111 -> 112...

Migration script to add the data_manager_history_association table and data_manager_job_association.

0112_add_data_manager_history_association_and_data_manager_job_association_tables DEBUG 2013-07-01 14:46:25,549 Created data_manager_history_association table
0112_add_data_manager_history_association_and_data_manager_job_association_tables DEBUG 2013-07-01 14:46:25,549 Created data_manager_history_association table
Created data_manager_history_association table
0112_add_data_manager_history_association_and_data_manager_job_association_tables DEBUG 2013-07-01 14:46:25,890 Created data_manager_job_association table
0112_add_data_manager_history_association_and_data_manager_job_association_tables DEBUG 2013-07-01 14:46:25,890 Created data_manager_job_association table
Created data_manager_job_association table
done
112 -> 113...

Migration script to update the migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate.

done
113 -> 114...

Migration script to update the migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate.

done
114 -> 115...
Altering password column failed
Traceback (most recent call last):
  File "lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py", line 15, in upgrade
    user.c.password.alter(type=String(255))
  File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/changeset/schema.py", line 491, in alter
    return alter_column(self, *p, **k)
  File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/changeset/schema.py", line 136, in alter_column
    engine._run_visitor(visitorcallable, delta)
  File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 2302, in _run_visitor
    conn._run_visitor(visitorcallable, element, **kwargs)
  File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1972, in _run_visitor
    **kwargs).traverse_single(element)
  File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/changeset/ansisql.py", line 53, in traverse_single
    ret = super(AlterTableVisitor, self).traverse_single(elem)
  File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/visitors.py", line 106, in traverse_single
    return meth(obj, **kw)
  File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/changeset/databases/sqlite.py", line 53, in visit_column
    self.recreate_table(table,column,delta)
  File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/changeset/databases/sqlite.py", line 36, in recreate_table
    self.execute()
  File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/changeset/ansisql.py", line 42, in execute
    return self.connection.execute(self.buffer.getvalue())
  File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1449, in execute
    params)
  File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1628, in _execute_text
    statement, parameters
  File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1698, in _execute_context
    context)
  File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1691, in _execute_context
    context)
  File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py", line 331, in do_execute
    cursor.execute(statement, parameters)
OperationalError: (OperationalError) there is already another table or index with this name: migration_tmp u'ALTER TABLE galaxy_user RENAME TO migration_tmp' ()
done
115 -> 116...

Tables for a next generation sequencing lims tied to requests.

Traceback (most recent call last):
  File "./scripts/manage_db.py", line 65, in <module>
    main( repository=repo, url=db_url )
  File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/shell.py", line 207, in main
    ret = command_func(**kwargs)
  File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/api.py", line 186, in upgrade
    return _migrate(url, repository, version, upgrade=True, err=err, **opts)
  File "<string>", line 2, in _migrate
  File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/util/__init__.py", line 159, in with_engine
    return f(*a, **kw)
  File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/api.py", line 366, in _migrate
    schema.runchange(ver, change, changeset.step)
  File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/schema.py", line 91, in runchange
    change.run(self.engine, step)
  File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/script/py.py", line 145, in run
    script_func(engine)
  File "lib/galaxy/model/migrate/versions/0116_seq_lims.py", line 52, in upgrade
    for table in _get_tables(metadata):
  File "lib/galaxy/model/migrate/versions/0116_seq_lims.py", line 34, in _get_tables
    primary_key = True),
  File "build/bdist.linux-x86_64/egg/sqlalchemy/schema.py", line 305, in __new__
sqlalchemy.exc.InvalidRequestError: Table 'sample_request_map' is already defined for this MetaData instance.  Specify 'extend_existing=True' to redefine options and columns on an existing Table object.
Error in sys.excepthook:
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/apport_python_hook.py", line 64, in apport_excepthook
    from apport.fileutils import likely_packaged, get_recent_crashes
ImportError: No module named apport.fileutils

Original exception was:
Traceback (most recent call last):
  File "./scripts/manage_db.py", line 65, in <module>
    main( repository=repo, url=db_url )
  File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/shell.py", line 207, in main
    ret = command_func(**kwargs)
  File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/api.py", line 186, in upgrade
    return _migrate(url, repository, version, upgrade=True, err=err, **opts)
  File "<string>", line 2, in _migrate
  File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/util/__init__.py", line 159, in with_engine
    return f(*a, **kw)
  File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/api.py", line 366, in _migrate
    schema.runchange(ver, change, changeset.step)
  File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/schema.py", line 91, in runchange
    change.run(self.engine, step)
  File "/home/galaxy/bin/chapman-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/script/py.py", line 145, in run
    script_func(engine)
  File "lib/galaxy/model/migrate/versions/0116_seq_lims.py", line 52, in upgrade
    for table in _get_tables(metadata):
  File "lib/galaxy/model/migrate/versions/0116_seq_lims.py", line 34, in _get_tables
    primary_key = True),
  File "build/bdist.linux-x86_64/egg/sqlalchemy/schema.py", line 305, in __new__
sqlalchemy.exc.InvalidRequestError: Table 'sample_request_map' is already defined for this MetaData instance.  Specify 'extend_existing=True' to redefine options and columns on an existing Table object.


On Mon, Jul 1, 2013 at 12:46 PM, Brad Chapman <chapmanb@50mail.com> wrote:

Lee;

> Hi, I would like to remove the "multiplexed" menu from the nglims sample
> information form.  How would I do that?  In our lab, we don't want
> submitters making their own libraries since they might accidentally use the
> same barcodes or somehow mess up others' libraries.  We want to remove that
> option altogether.

Good idea. I added a flag to the nglims.yaml file so you can specify
whether barcode multiplexing is available or not:

https://bitbucket.org/chapmanb/galaxy-central/src/62f7dc3864535e68af7aa2a7ef0c37e45eb9707a/tool-data/nglims.yaml?at=default#cl-97

setting `available: false` will turn off the option for the user to
select and add this.

If you update from the latest in bitbucket it will have this change. I
also synchronized with the most recent galaxy-dist, so an update will
pull in those changes as well.

> Actually along the same lines, we would like to remove all "services
> needed" check boxes too and simply have all of the data entry on one page.

Moving to a single page entry would be a big change from the current
wizard approach. You can control what services are available by default
using the `default` flag in the nglims.yaml:

https://bitbucket.org/chapmanb/galaxy-central/src/62f7dc3864535e68af7aa2a7ef0c37e45eb9707a/tool-data/nglims.yaml?at=default#cl-133

Currently sequencing is the only one selected by default but you can add
others if they're commonly used to make the submission process easier
for users.

Hope this helps,
Brad



--
Lee Katz, Ph.D.