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.
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>'
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