Hi, I noticed some chances in the repository which give the following error. sudo python scripts/nglims/add_ng_defaults.py universe_wsgi.ini Traceback (most recent call last): File "scripts/nglims/add_ng_defaults.py", line 43, in <module> import galaxy.model.mapping File "/opt/glims/galaxy-central/lib/galaxy/model/__init__.py", line 10, in <module> from galaxy.util.bunch import Bunch File "/opt/glims/galaxy-central/lib/galaxy/util/__init__.py", line 485, in <module> os.path.join(shared_dir, "ucsc", "top_builds.txt")) File "/opt/glims/galaxy-central/lib/galaxy/util/__init__.py", line 322, in read_dbnames for line in open(filename): IOError: [Errno 2] No such file or directory: '/opt/glims/galaxy-central/lib/galaxy/util/../../../tool-data/shared/ucsc/builds.txt' I also see the error below when trying to start galaxy. Thanks in advance. Victor galaxy-central > ./run.sh Some eggs are out of date, attempting to fetch... Fetched http://eggs.g2.bx.psu.edu/new/Mako/Mako-0.2.5-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/Babel/Babel-0.9.4-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/Whoosh/Whoosh-0.3.18-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/Tempita/Tempita-0.1-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/Cheetah/Cheetah-2.2.2-py2.5-linux-x86_64-ucs2.... Fetched http://eggs.g2.bx.psu.edu/new/lrucache/lrucache-0.2-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/boto/boto-1.8d-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/NoseHTML/NoseHTML-0.3.1-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/pexpect/pexpect-2.4-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/bx_python/bx_python-0.5.0_dev_f74aec067563-py2... Fetched http://eggs.g2.bx.psu.edu/new/PasteDeploy/PasteDeploy-1.3.3-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/WebHelpers/WebHelpers-0.2-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/numpy/numpy-1.3.0-py2.5-linux-x86_64-ucs2.egg Fetched http://eggs.g2.bx.psu.edu/new/pysqlite/pysqlite-2.5.6_3.6.17_static-py2.5-li... Fetched http://eggs.g2.bx.psu.edu/new/Beaker/Beaker-1.4-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/SVGFig/SVGFig-1.1.6-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/simplejson/simplejson-2.1.1-py2.5-linux-x86_64... Fetched http://eggs.g2.bx.psu.edu/new/WebError/WebError-0.8a-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/python_lzo/python_lzo-1.08_2.03_static-py2.5-l... Fetched http://eggs.g2.bx.psu.edu/new/twill/twill-0.9-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/Routes/Routes-1.12.3-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/decorator/decorator-3.1.2-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/sqlalchemy_migrate/sqlalchemy_migrate-0.5.4-py... Fetched http://eggs.g2.bx.psu.edu/new/GeneTrack/GeneTrack-2.0.0_beta_1_dev_48da9e998... Fetched http://eggs.g2.bx.psu.edu/new/pycrypto/pycrypto-2.0.1-py2.5-linux-x86_64-ucs... Fetched http://eggs.g2.bx.psu.edu/new/Paste/Paste-1.6-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/nose/nose-0.11.1-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/amqplib/amqplib-0.6.1-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/WebOb/WebOb-0.8.5-py2.5.egg Fetched http://eggs.g2.bx.psu.edu/new/PasteScript/PasteScript-1.7.3-py2.5.egg Fetch successful. python path is: /opt/glims/galaxy-central/eggs/Whoosh-0.3.18-py2.5.egg, /opt/glims/galaxy-central/eggs/pycrypto-2.0.1-py2.5-linux-x86_64-ucs2.egg, /opt/glims/galaxy-central/eggs/python_lzo-1.08_2.03_static-py2.5-linux-x86_64-ucs2.egg, /opt/glims/galaxy-central/eggs/bx_python-0.5.0_dev_f74aec067563-py2.5-linux-x86_64-ucs2.egg, /opt/glims/galaxy-central/eggs/amqplib-0.6.1-py2.5.egg, /opt/glims/galaxy-central/eggs/pexpect-2.4-py2.5.egg, /opt/glims/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg, /opt/glims/galaxy-central/eggs/Babel-0.9.4-py2.5.egg, /opt/glims/galaxy-central/eggs/Beaker-1.4-py2.5.egg, /opt/glims/galaxy-central/eggs/Mako-0.2.5-py2.5.egg, /opt/glims/galaxy-central/eggs/WebHelpers-0.2-py2.5.egg, /opt/glims/galaxy-central/eggs/simplejson-2.1.1-py2.5-linux-x86_64-ucs2.egg, /opt/glims/galaxy-central/eggs/wchartype-0.1-py2.5.egg, /opt/glims/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.5.egg, /opt/glims/galaxy-central/eggs/docutils-0.4-py2.5.egg, /opt/glims/galaxy-central/eggs/WebOb-0.8.5-py2.5.egg, /opt/glims/galaxy-central/eggs/Routes-1.12.3-py2.5.egg, /opt/glims/galaxy-central/eggs/Cheetah-2.2.2-py2.5-linux-x86_64-ucs2.egg, /opt/glims/galaxy-central/eggs/PasteDeploy-1.3.3-py2.5.egg, /opt/glims/galaxy-central/eggs/PasteScript-1.7.3-py2.5.egg, /opt/glims/galaxy-central/eggs/Paste-1.6-py2.5.egg, /opt/glims/galaxy-central/lib, /usr/local/lib/python2.5/site-packages/setuptools-0.6c11-py2.5.egg, /usr/local/lib/python2.5/site-packages/rpy2-2.1.5_20101007-py2.5-linux-x86_64.egg, /usr/local/lib/python25.zip, /usr/local/lib/python2.5, /usr/local/lib/python2.5/plat-linux2, /usr/local/lib/python2.5/lib-tk, /usr/local/lib/python2.5/lib-dynload, /usr/local/lib/python2.5/site-packages Traceback (most recent call last): File "/opt/glims/galaxy-central/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/opt/glims/galaxy-central/lib/galaxy/app.py", line 19, in __init__ self.config.check() File "/opt/glims/galaxy-central/lib/galaxy/config.py", line 161, in check raise ConfigurationError("Directory does not exist: %s" % path ) ConfigurationError: Directory does not exist: ./database/files On Oct 8, 2010, at 9:23 AM, Nate Coraor wrote:
Victor Ruotti wrote:
Thanks Brad. Did an hq pull and hq update.
Looks like its looking for the file_path. Do I set this in the universe_wsgi.ini and what should I set to? thanks Victor
galaxy-central > sudo python scripts/nglims/add_ng_defaults.py universe_wsgi.ini Traceback (most recent call last): File "scripts/nglims/add_ng_defaults.py", line 367, in <module> main(*args) File "scripts/nglims/add_ng_defaults.py", line 62, in main app = SimpleApp(db_con, config['file_path']) KeyError: 'file_path'
Just a heads up to Brad,
I recently changed galaxy.config so that almost everything that was "set" in universe_wsgi.ini was correctly defined as a default in the config, and then I commented out all of those values. The hope is that it makes it easier to maintain your config file against the sample as the sample changes over time. However, it means that a lot of the things your script expects to be defined aren't defined, so you may need to load galaxy.config yourself to access the defaults.
--nate
On Oct 8, 2010, at 6:55 AM, Brad Chapman wrote:
Victor;
Using the central repository with a newer version of python and the virtual env Peter suggested all worked out great.
I was able to create a request form and sample form from the admin section. Now I can create a new sequencing request and use it to add samples etc. All this looked very good!
Awesome. Great to hear it.
Now when I do this 3. Add configured request types, forms and sample states to the database:
$ python scripts/nglims/add_ng_defaults.py universe_wsgi.ini I get,
galaxy-central > sudo python scripts/nglims/add_ng_defaults.py universe_wsgi.ini Traceback (most recent call last): File "scripts/nglims/add_ng_defaults.py", line 363, in <module> main(*args) File "scripts/nglims/add_ng_defaults.py", line 57, in main db_con = "sqlite:///%s?isolation_level=IMMEDIATE" % config["database_file"] KeyError: 'database_file'
It looks like database_connection isn't set in your universe_wsgi.ini. If you update the repository (hg pull; hg update) or grab the latest script I added a fix for this case:
http://bitbucket.org/chapmanb/galaxy-central/src/tip/scripts/nglims/add_ng_d...
You may also want to explicitly set the connection in the configuration file as a more general solution.
Let us know if you run into any other problems. Thanks much, Brad _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
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