biosql_pyramid

Fork of https://github.com/chapmanb/biosqlweb which was build using pylons. This project is ported to pyramid so you can run it locally without Google Apps Engine

Setup

1. Clone repo

$> git clone https://github.com/VDBWRAIR/biosql_pyramid
$> cd biosql_pyramid

2. Get virtualenv setup(Optional, but recommended)

$> virtualenv .
$> . bin/activate

3. Install project and all dependencies

$> python setup.py install

4. Initialize database

$> ./initdb.py

5. Load some data from GenBank

Create file called accession.lst with gi numbers or accessions(one per line) There is an example included with the following content

KF824902
KF824903
JF504679

Load it up

$> ./loadseqs.py accessions.lst

6. Startup the server and have it open up browser

pserve development.ini -b

Summary page

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