Waldo: Where Proteins Are
Waldo tells what everyone already knows.
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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
You can run the
install.sh file to get everything working:
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
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):
--user(the default for
install.sh) installs waldo locally for this user (under
- Without an argument, it installs it system-wide (you need to have write
- You can specify exactly where to store the data.
datadir is where waldo will store the downloaded information. It
/var/lib/waldo/data. You can also specify where to store the
database file (default is
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:
Then point your browser to http://localhost:8000/