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Installation

  • Windows Xampp All-In-One Version

    • Short instructions:

    1) Unzip xampplite-plasmidb_all-in-one.zip in C:\.
    Plasmi::db is now installed!

    Detailed instructions:

    1) Download xampplite-plasmidb_all-in-one.zip
    2) Unzip the file plasmidb-xampplite-all_in_one.zip in C:\
    3) Go to C:\xampplite
    4) Click on xampp-control (Fig1.png)
    5) The control panel should open. Click on "start" for apache and for Mysql (Fig2.png).
    6) Go to http://localhost/plasmidb/
    7) Log in with the username: "test@example.com", password: "password". Everything should now work (Fig3.png)
    (The database is empty apart from one item I added just to show you how it works.)

  • Unix / Linux / MacOS X

    • Download the latest release, consisting of a the PHP web interface and SQL to provide the underlying database. 

    Short Instructions

    1) You can find the PHP web interface here: Plasmidb-0.9.1.zip

    2) Download the empty database, which is here: plasmidb.sql

    3) Untar the web interface & put it under your Apache DOCUMENT_ROOT, for example: 
    % tar -zxvf Plasmidb-0.9.1.zip
% mv Plasmidb/* /var/www/html
    4) Install the MySQL database & make sure its running (see below for more detailed instructions)

    5) Install the SQL database:
    % mysql -u root
mysql> CREATE DATABASE plasmidb2_development;
mysql> quit;
% mysql -u root -c plasmidb2_development < plasmidb.sql

    6) Create plasmidb users with passwords (e.g. using PHPMyAdmin).
    There is a 'guest' user with password 'guest' in the example database.

    7) Check the file "plasmidb/config/db.conf" and "plasmidb/config/app.conf" to make sure the passwords and directories are set up properly

    8) Install PEAR packages from the command line: 
    $ sudo pear help 
$ sudo pear channel-update pear.php.net
$ sudo pear install DB # things should downloading and installing automatically
$ sudo pear install DB_DataObject
$ sudo pear install HTML_Table
$ sudo pear install HTML_QuickForm

    9) Browse to http://localhost/plasmidb/ to log in and start adding information.

    Long Instructions

    Install the web server, php and mod_php

    $ apt-get install php5-cli php-pear php5 php5-mysqli php5-common libapache2-mod-php5 mysql-server

    Install PEAR components (http:\\pear.php.net\)

    $ sudo pear help # allows us to see how to get started
$ sudo pear channel-update pear.php.net 
$ sudo pear install DB # things should downloading and installing automatically
$ sudo pear install DB_DataObject
$ sudo pear install HTML_Table
$ sudo pear install HTML_QuickForm

    Download everything (from CVS this time!)

    $ sudo apt-get install cvs
$ cvs -d:pserver:anonymous@plasmidb.cvs.sourceforge.net:/cvsroot/plasmidb login
$ cvs -z3 -d:pserver:anonymous@plasmidb.cvs.sourceforge.net:/cvsroot/plasmidb co -P plasmidb
$ cvs -z3 -d:pserver:anonymous@plasmidb.cvs.sourceforge.net:/cvsroot/plasmidb co -P Phly
$ cvs -z3 -d:pserver:anonymous@plasmidb.cvs.sourceforge.net:/cvsroot/plasmidb co -P Bio
$ cvs -z3 -d:pserver:anonymous@plasmidb.cvs.sourceforge.net:/cvsroot/plasmidb co -P Html
$ cd plasmidb/config
$ vi db.conf # Set up your DB information & password here
$ vi app.conf # Check that the directories are set up OK

    Set up the DB in MySQL

    $ mysql -u root
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 7 to server version: 5.0.22-Debian_0ubuntu6.06.2-log

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> create DATABASE plasmidb2_development;
Query OK, 1 row affected (0.02 sec)

mysql> Bye # Control-D exits mysql

$mysql -u root  plasmidb2_development < ~/plasmidb_dev.sql

    If you have problems installing PEAR components, here is a good introduction from O'Reilly.