tools for running phred(need to change path later), trim sequence, generate boxplot and an array of length of the reads.
test data are added.
trim sequence and array of length passed functional test.
phred (2 ouput files) and boxplot (pdf file) didn't pass functional test yet.
For example you can do:
database_connection = postgres:///galaxy_test
database_engine_option_echo = true
database_engine_option_echo_pool = true
database_engine_option_pool_size = 30
To increase the pool size to 30 and turn on SQL and Pool debug echoing
The main worry here is that substantial changes have been made to the
how the HTTP server / threadpool work so we should run this in test for a
while and hit it with the load tests.
Also, now using WebError for the interactive exception debugging, it has many
more features including much better formatting of errors in Mako templates.
Added some new eggs that Paste/WebError depend on: wsgiref, WebOb, and Tempita.
It won't work with the current logic in lib/galaxy/model/mapping.py fixed in this revision
(Note the wierd traceback below - looking in build/bdist.macosx-10.3-fat/egg/sqlalchemy/schema.py on a linux box!?)
[rerla@hg rgalaxy_svn]$ sh run.sh
Architecture appears to be linux-x86_64 UCS4
python path: /home/rerla/rgalaxy_svn/lib:/home/rerla/rgalaxy_svn/eggs/UCS4:/home/rerla/rgalaxy_svn/eggs
python path is: /home/rerla/rgalaxy_svn/scripts, /usr/local/lib/python2.4/site-packages/setuptools-0.6c6-py2.4.egg, /home/rerla/rgalaxy_svn/lib,
/home/rerla/rgalaxy_svn/eggs/UCS4/Cheetah-1.0-py2.4-linux-x86_64.egg, /home/rerla/rgalaxy_svn/eggs/UCS4/bx_python-0.5.0_dev-py2.4-linux-x86_64.egg,
/home/rerla/rgalaxy_svn/eggs/UCS4/pysqlite-2.3.5_3.4.2_static-py2.4-linux-x86_64.egg,
/home/rerla/rgalaxy_svn/eggs/UCS4/psycopg2-2.0.6_8.2.4_static-py2.4-linux-x86_64.egg, /home/rerla/rgalaxy_svn/eggs/UCS4,
/home/rerla/rgalaxy_svn/eggs/PasteScript-1.0-py2.4.egg, /home/rerla/rgalaxy_svn/eggs/PasteDeploy-1.0-py2.4.egg,
/home/rerla/rgalaxy_svn/eggs/Paste-1.0-py2.4.egg, /home/rerla/rgalaxy_svn/eggs/Routes-1.6.3-py2.4.egg,
/home/rerla/rgalaxy_svn/eggs/flup-0.5.dev_r2311-py2.4.egg, /home/rerla/rgalaxy_svn/eggs/docutils-0.4-py2.4.egg,
/home/rerla/rgalaxy_svn/eggs/elementtree-1.2.6_20050316-py2.4.egg, /home/rerla/rgalaxy_svn/eggs/WebHelpers-0.2-py2.4.egg,
/home/rerla/rgalaxy_svn/eggs/simplejson-1.4-py2.4.egg, /home/rerla/rgalaxy_svn/eggs/Mako-0.1.8-py2.4.egg, /home/rerla/rgalaxy_svn/eggs/Beaker-0.5-py2.4.egg,
/home/rerla/rgalaxy_svn/eggs/MyghtyUtils-0.52-py2.4.egg, /home/rerla/rgalaxy_svn/eggs/SQLAlchemy-0.3.11-py2.4.egg, /home/rerla/rgalaxy_svn/eggs,
/usr/local/lib/python24.zip, /usr/local/lib/python2.4, /usr/local/lib/python2.4/plat-linux2, /usr/local/lib/python2.4/lib-tk,
/usr/local/lib/python2.4/lib-dynload, /usr/local/lib/python2.4/site-packages, /usr/local/lib/python2.4/site-packages/Numeric,
/usr/local/lib/python2.4/site-packages/PIL
Traceback (most recent call last):
File "./scripts/paster.py", line 7, in ?
command.run()
File "/home/rerla/rgalaxy_svn/eggs/PasteScript-1.0-py2.4.egg/paste/script/command.py", line 76, in run
File "/home/rerla/rgalaxy_svn/eggs/PasteScript-1.0-py2.4.egg/paste/script/command.py", line 115, in invoke
File "/home/rerla/rgalaxy_svn/eggs/PasteScript-1.0-py2.4.egg/paste/script/command.py", line 210, in run
File "/home/rerla/rgalaxy_svn/eggs/PasteScript-1.0-py2.4.egg/paste/script/serve.py", line 184, in command
File "/home/rerla/rgalaxy_svn/eggs/PasteScript-1.0-py2.4.egg/paste/script/serve.py", line 204, in loadapp
File "/home/rerla/rgalaxy_svn/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 193, in loadapp
File "/home/rerla/rgalaxy_svn/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 214, in loadobj
File "/home/rerla/rgalaxy_svn/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 596, in create
File "/home/rerla/rgalaxy_svn/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 99, in invoke
File "/home/rerla/rgalaxy_svn/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call
File "/home/rerla/rgalaxy_svn/lib/galaxy/web/buildapp.py", line 56, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File "/home/rerla/rgalaxy_svn/lib/galaxy/app.py", line 23, in __init__
create_tables = True )
File "/home/rerla/rgalaxy_svn/lib/galaxy/model/mapping.py", line 297, in init
metadata.create_all()
File "build/bdist.macosx-10.3-fat/egg/sqlalchemy/schema.py", line 1238, in create_all
File "build/bdist.macosx-10.3-fat/egg/sqlalchemy/schema.py", line 1274, in _get_engine
sqlalchemy.exceptions.InvalidRequestError: This SchemaItem is not connected to any Engine or Connection.
Greg Von Kuster