February 2007 - galaxy-user - lists.galaxyproject.org

New tools available on Galaxy
by yizhang＠bx.psu.edu 20 Feb '07

20 Feb '07

New tools released to Galaxy Test at http://test.g2.bx.psu.edu. 1. Gene BED to Exon/Intron BED ("Convert Formats" tool set) - This tool is an enhancement to the old tool "Gene BED to Exon BED". It converts a UCSC gene bed format file to a list of bed format lines corresponding to requested features of each gene. The new feature is to convert gene bed lines to intron bed lines. And the interface is more user friendly. 2. yn00 ("PAML" tool set) - this tool finds the ratio of the number of non-synonymous substitutions per non-synonymous site (Ka) to the number of synonymous substitutions per synonymous site (Ks) for the alignments in the input file.

1 0

Install problem: SQLite DBAPI not found
by Thomas Junier 16 Feb '07

16 Feb '07

Hi folks, First of all, I'm not sure if this is the right list to post to, so my apologies if it isn't. I'm trying to install Galaxy on my machine, according to the instructions at http://g2.trac.bx.psu.edu/wiki/HowToInstall. Everything works fine until I try to do: $ sh run.sh at which point I get a Python traceback in which the last call raises the following error: File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.3.3-py2.4.egg/sqlalchemy/engine/strategies.py", line 52, in create sqlalchemy.exceptions.InvalidRequestError: Cant get DBAPI module for dialect '<sqlalchemy.databases.sqlite.SQLiteDialect object at 0x2a983a6fd0>' (whole traceback at end of mail) I'm using Python version 2.4.3. on a Linux box (SuSE 9) The eggs/ directory does contain a bunch of pysqlite*.egg files, but apparently Python can't find them or else they're not the right ones, or whatnot. Is there a step I missed during install? Any other ideas? Thanks in advance. Thomas ------------ Whole traceback: $ sh run.sh Architecture appears to be linux-x86_64 python path: /home/galaxy/galaxy_dist/lib:/home/galaxy/galaxy_dist/eggs Traceback (most recent call last): File "./scripts/paster.py", line 7, in ? command.run() File "/home/galaxy/galaxy_dist/eggs/PasteScript-1.0-py2.4.egg/paste/script/command.py", line 76, in run File "/home/galaxy/galaxy_dist/eggs/PasteScript-1.0-py2.4.egg/paste/script/command.py", line 115, in invoke File "/home/galaxy/galaxy_dist/eggs/PasteScript-1.0-py2.4.egg/paste/script/command.py", line 210, in run File "/home/galaxy/galaxy_dist/eggs/PasteScript-1.0-py2.4.egg/paste/script/serve.py", line 184, in command File "/home/galaxy/galaxy_dist/eggs/PasteScript-1.0-py2.4.egg/paste/script/serve.py", line 204, in loadapp File "/home/galaxy/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 193, in loadapp File "/home/galaxy/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 214, in loadobj File "/home/galaxy/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 596, in create File "/home/galaxy/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 96, in invoke File "/home/galaxy/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call File "/home/galaxy/galaxy_dist/eggs/Paste-1.0-py2.4.egg/paste/urlmap.py", line 24, in urlmap_factory File "/home/galaxy/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 281, in get_app File "/home/galaxy/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 596, in create File "/home/galaxy/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 99, in invoke File "/home/galaxy/galaxy_dist/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call File "/home/galaxy/galaxy_dist/lib/galaxy/app.py", line 48, in app_factory app = UniverseApplication( **kwargs ) File "/home/galaxy/galaxy_dist/lib/galaxy/app.py", line 23, in __init__ create_tables = True ) File "/home/galaxy/galaxy_dist/lib/galaxy/model/mapping.py", line 201, in init metadata.connect( url, **kwargs ) File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.3.3-py2.4.egg/sqlalchemy/schema.py", line 936, in connect File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.3.3-py2.4.egg/sqlalchemy/engine/__init__.py", line 91, in create_engine File "/home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.3.3-py2.4.egg/sqlalchemy/engine/strategies.py", line 52, in create sqlalchemy.exceptions.InvalidRequestError: Cant get DBAPI module for dialect '<sqlalchemy.databases.sqlite.SQLiteDialect object at 0x2a983a6fd0>'

1 0

News From the Galaxy Development Team
by yizhang＠bx.psu.edu 09 Feb '07

09 Feb '07

Hello Galaxy Users, The Galaxy development team is starting a new initiative for communicating important announcements about Galaxy to our users. We will be sending announcements like this one to the galaxy-user(a)bx.psu.edu email list, so if you are interested in receiving these announcements, please be sure to subscribe to this list. We are also in the process of adding a "News" page to our Galaxy wiki documentation, so some announcements will be available there as well. Here are the highlights of the new features that are currently available on our Galaxy test environment at http://test.g2.bx.psu.edu/. Maf Limit to Species Tool This tool offers the ability to remove any undesired species from a MAF file. Columns which contain only gaps are removed. The user can choose to keep or discard blocks which do not have all the desired species. The user can also choose to include blocks which contain only a single species. Enhanced LAJ Tool We have added a dialog box for filtering the input data. This eliminates a problem we were having with integer overflow. Enhanced Build Lists of the Upload Tool and Edit Attributes Build lists are now alphabetized (by display name) in edit attributes and the upload tool. Miscellaneous We have made several miscellaneous improvements throughout the application, including (but not limited to) better descriptions of errors encountered with invalid data source files (even more improvements coming in this area). As stated above, we'll continue to contact you with new about important Galaxy enhancements and updates. Thanks very much, The Galaxy Development Team

1 0