- Requirements
-
Python 2.7+ with modules:
- biopython
- matplotlib
- mysqldb
- networkx
- openpyxl 1.9+
- webcolors
-
MySQL 5.5+
-
optional: libSBML 5.10+ built with python API (requirements: swig, libxml2)
Suggested command(s) for installation on Ubuntu 14.04
$ sudo apt-get install build-essential mysql-server python-biopython \
python-webcolors python-networkx python-mysqldb python-matplotlib \
libxml2 libxml2-dev python-dev python-pip zlib1g zlib1g-dev bzip2 libbz2-dev
$ sudo pip install python-libsbml
$ sudo pip install openpyxl
- Suggestions
-
phpmyadmin (to more easily inspect database)
-
optional: Grant FILE permissions to database user
Note: Mysql clients connecting to the database server need to enable infile_local to make use of the above!Suggested command(s) for installation on Ubuntu 14.04
$ sudo apt-get install phpmyadmin
$ mysql -u root -p
> GRANT FILE ON *.* TO <user>@'%';
> quit
Call ./miRwb.py -h
to get an overview of the possible options.
At the moment, it is possible to
- run a database update (-u, (re)parses files in the (data/db_files)[data/db_files], but does not download new ones),
- reconstruct interaction networks from scratch (option -b/-B),
- convert CellDesigner files to GML (option -p),
- expand existing networks (more involved commands).
Before you start, you have to acquire the desired database files from their respective origin and set up the database in MySQL. There is a file called database_schema.sql
in the repository's root directory which you can use to get the database skeleton like this:
$ mysql -u <user> -p BioNetworks < database_schema.sql