https://github.com/luispedro/waldo
Waldo Project
https://github.com/luispedro/waldo
Last synced: 12 months ago
JSON representation
Waldo Project
- Host: GitHub
- URL: https://github.com/luispedro/waldo
- Owner: luispedro
- License: mit
- Created: 2009-09-29T17:32:19.000Z (over 16 years ago)
- Default Branch: master
- Last Pushed: 2015-10-20T16:41:34.000Z (over 10 years ago)
- Last Synced: 2025-05-10T21:35:06.511Z (about 1 year ago)
- Language: Python
- Homepage:
- Size: 3.75 MB
- Stars: 2
- Watchers: 5
- Forks: 3
- Open Issues: 11
-
Metadata Files:
- Readme: README.rst
- License: COPYING.MIT
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README
Waldo: Where Proteins Are
-------------------------
Waldo tells what everyone already knows.
We have a manuscript in preparation. If you use this in a publication, please
let us know so we can (to the best of our knowledge), give you the right
citation.
Installation
............
Dependencies
~~~~~~~~~~~~
- python
- lxml
- sqlalchemy
- bottle
bottle is only needed if wish to run the web application (i.e., if you only
using the local programming API, then you can skip this step).
Under a debian or Ubuntu system, the following commands will install all needed
packages::
sudo apt-get install python-lxml
sudo apt-get install python-sqlalchemy
sudo apt-get install python-bottle
Installation
~~~~~~~~~~~~
You can run the ``install.sh`` file to get everything working::
./install.sh
The individual steps are::
python setup.py install
This is the standard Python installation command. In order to start using
waldo, you need to download all the database files and build the index. The
utility script ``update-waldo`` should accomplish this::
update-waldo --user
update-waldo
update-waldo --datadir /path/to/datadir --database database.sqlite3
There are three variations (shown above):
1. ``--user`` (the default for ``install.sh``) installs waldo locally for this
user (under ``$HOME/.local/share/waldo``)
2. Without an argument, it installs it system-wide (you need to have write
access to ``/var/lib/waldo``
3. You can specify exactly where to store the data.
The ``datadir`` is where waldo will store the downloaded information. It
defaults to ``/var/lib/waldo/data``. You can also specify where to store the
database file (default is ``/var/lib/waldo/waldo.sqlite3``).
Additionally, you can use the ``--unsafe`` flag to speed up the indexing, but
if you interrupt the process, the database may be broken::
update-waldo --user --unsafe
Running the Webapp
..................
If you have installed waldo as above, you should execute::
python woof/woof.py
Then point your browser to http://localhost:8000/
Links
.....
- documentation: http://waldo.readthedocs.org/en/latest/
- github: https://github.com/luispedro/waldo