Re: [galaxy-dev] OS X dev build attempt
Dear colleagues, I'm attempting to install a local instance of Galaxy for development purposes on my Mac. The Galaxy build script issued the following warning:
Your platform (py2.5-macosx-10.6-i386-ucs2) is not supported. Pre-built galaxy eggs are not available from the Galaxy developers for your platform. You may be able to build them by hand with: python scripts/scramble.py
Upon running scramble.py, it turned out that the link to pysqlite in eggs.ini is broken: http://initd.org/pub/software/pysqlite/releases/2.3/2.3.5/pysqlite-2.3.5.tar... so I replaced the corresponding line in the eggs.ini file with: http://pysqlite.googlecode.com/files/pysqlite-2.5.5.tar.gz http://www.sqlite.org/sqlite-source-3_5_4.zip (I haven't yet located a link to pysqlite 2.3.5 on the web.) This immediately created a problem with SQLAlchemy and sqlalchemy_migrate:
File "/Users/apoon/Source/galaxy/eggs/py2.5-noplatform/ SQLAlchemy-0.4.7p1-py2.5.egg/sqlalchemy/engine/base.py", line 942, in _handle_dbapi_exception raise exceptions.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) ProgrammingError: (ProgrammingError) Cannot operate on a closed cursor. None None Googled the respective error messages and found that there's a version conflict with pysqlite 2.5.5. So those got updated as well, with the corresponding line edits to eggs.ini.
So far so good. But then run.sh exited with another problem:
File "lib/galaxy/model/migrate/versions/ 0005_cleanup_datasets_fix.py", line 665, in upgrade for dataset in context.query( Dataset ).filter( and_ ( Dataset.c.deleted == True, Dataset.c.purged == False ) ): AttributeError: type object 'Dataset' has no attribute 'c'
I poked around in that script and found that while class Dataset has no attribute 'c', it sure has attributes 'deleted' and 'purged'. So I changed that line to:
for dataset in context.query( Dataset ).filter( and_ ( Dataset.deleted == True, Dataset.purged == False ) ):
Re-ran run.sh, got asked to migrate the database scheme, so sh manage_db.sh upgrade it is, followed with another run.sh and hey, presto! My Mac is running Galaxy. ^_^ Cheers, - Art.
Art, thanks very much for this information - we'll look at upgrading pysqlite from 2.3.5 to 2.5.5. Regarding the following issue:
So far so good. But then run.sh exited with another problem:
File "lib/galaxy/model/migrate/versions/ 0005_cleanup_datasets_fix.py", line 665, in upgrade for dataset in context.query( Dataset ).filter( and_ ( Dataset.c.deleted == True, Dataset.c.purged == False ) ): AttributeError: type object 'Dataset' has no attribute 'c'
This code was changed to work with sqlalchemy 0.5 in change set 2909, so the latest rev includes the correct query. Greg Von Kuster On Nov 6, 2009, at 7:47 PM, Art Poon wrote:
Dear colleagues,
I'm attempting to install a local instance of Galaxy for development purposes on my Mac. The Galaxy build script issued the following warning:
Your platform (py2.5-macosx-10.6-i386-ucs2) is not supported. Pre-built galaxy eggs are not available from the Galaxy developers for your platform. You may be able to build them by hand with: python scripts/scramble.py
Upon running scramble.py, it turned out that the link to pysqlite in eggs.ini is broken: http://initd.org/pub/software/pysqlite/releases/2.3/2.3.5/ pysqlite-2.3.5.tar.gz
so I replaced the corresponding line in the eggs.ini file with: http://pysqlite.googlecode.com/files/pysqlite-2.5.5.tar.gz http:// www.sqlite.org/sqlite-source-3_5_4.zip
(I haven't yet located a link to pysqlite 2.3.5 on the web.)
This immediately created a problem with SQLAlchemy and sqlalchemy_migrate:
File "/Users/apoon/Source/galaxy/eggs/py2.5-noplatform/ SQLAlchemy-0.4.7p1-py2.5.egg/sqlalchemy/engine/base.py", line 942, in _handle_dbapi_exception raise exceptions.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) ProgrammingError: (ProgrammingError) Cannot operate on a closed cursor. None None Googled the respective error messages and found that there's a version conflict with pysqlite 2.5.5. So those got updated as well, with the corresponding line edits to eggs.ini.
So far so good. But then run.sh exited with another problem:
File "lib/galaxy/model/migrate/versions/ 0005_cleanup_datasets_fix.py", line 665, in upgrade for dataset in context.query( Dataset ).filter( and_ ( Dataset.c.deleted == True, Dataset.c.purged == False ) ): AttributeError: type object 'Dataset' has no attribute 'c'
I poked around in that script and found that while class Dataset has no attribute 'c', it sure has attributes 'deleted' and 'purged'. So I changed that line to:
for dataset in context.query( Dataset ).filter( and_ ( Dataset.deleted == True, Dataset.purged == False ) ):
Re-ran run.sh, got asked to migrate the database scheme, so sh manage_db.sh upgrade it is, followed with another run.sh and hey, presto! My Mac is running Galaxy. ^_^
Cheers, - Art.
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Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster wrote:
This code was changed to work with sqlalchemy 0.5 in change set 2909, so the latest rev includes the correct query.
And I would suggest upgrading ASAP - there were many other SQLAlchemy 0.5 fixes included that are included that you'll need. --nate
Curses! My tarball was 2 weeks too stale :-( Thanks for the heads-up :-) - Art. On Nov 9, 2009, at 6:35 AM, Nate Coraor wrote:
Greg Von Kuster wrote:
This code was changed to work with sqlalchemy 0.5 in change set 2909, so the latest rev includes the correct query.
And I would suggest upgrading ASAP - there were many other SQLAlchemy 0.5 fixes included that are included that you'll need.
--nate
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Art Poon -
Art Poon -
Greg Von Kuster -
Nate Coraor