From c7127ff5440529dd4bad599c843d2cce3cacf585 Mon Sep 17 00:00:00 2001 From: chenry Date: Thu, 29 Sep 2011 12:49:48 -0500 Subject: [PATCH] Changing the instructions to point at our web pages... so we're not maintaining instructions in two places. --- Configuration Instructions.txt | 51 +-------------------- Linux and OSX Installation Instructions.txt | 14 +----- 2 files changed, 4 insertions(+), 61 deletions(-) diff --git a/Configuration Instructions.txt b/Configuration Instructions.txt index a0ae256..884a5cd 100644 --- a/Configuration Instructions.txt +++ b/Configuration Instructions.txt @@ -1,49 +1,2 @@ -Once the Model SEED has been successfully installed, you must configure it to your running environment, and you must install the data associated with the Model SEED -1.) Customize the Model SEED configuration file - a.) Copy the default configuration file Model-SEED-core/config/Settings.config to a new filename (e.g. MyModelSEED.config): - b.) Edit you new configuration file filling in the following parameters (ignore the others for now): - [Optional] - SeedUsername=(your SEED account username) - SeedPassword=(your SEED account password) - dataDirectory=(location where your extracted the Model SEED flatfiles in step 1) - [Optimizers] - directoryGLPK=(location where glpk has been installed on your system) - includeDirectoryCPLEX=(location where cplex include files are located if you have cplex, leave commented otherwise) - libraryDirectoryCPLEX=(location where cplex library files are located if you have cplex, leave commented otherwise) - licenceDirectoryCPLEX=(location of cplex license file if you have cplex, leave commented otherwise) -2.) Decide upon the database backend: either MySQL or SQL-lite - a.) The Model SEED can use two different database implementations to store the relational database that comes with the Model SEED - -MySQL: a heavy weight implementation with a separate installation that provides enhanced performance for heavy-duty use - -SQL-lite: a light weight implementation built into Model SEED, requiring no effort to install or configure, but delivering reduced performance - b.) By default, Model SEED assumes an SQL-lite database backend because this provides us with an easier installation process. If you're using SQL-lite, JUMP TO STEP (4) - c.) If you're using MySQL, JUMP TO STEP (3) -3.) Install and load MySQL database - a.) Set up an SQL server on your computer or identify a server with SQL that you have access to - b.) Create or identify a user account in the SQL server that Model SEED can use to interact with the server, and give this user account privileges to make schemes. - c.) Adjust database parameters in config file - [Database] - # type is either sqlite or mysql - type=(set this to "mysql") - # required for mysql - username=(set to username for Model SEED account in MySQL database) - password=(set to password for Model SEED account in MySQL database, leave commented if no password) - host=(set to host location of computer where database is hosted, "localhost" if on local machine) - socket=(points to location of MySQL ".sock" file) (on OSX it is usually /tmp/mysql.sock) - port=(set to port for MySQL database, defaults to 3306 if left commented) - d.) Run this command: Model-SEED-core/bin/ms-config load "Name of your config file that you filled out in steps 2.b and 3.c" - e.) Run this script: Model-SEED-core/bin/CreateDBScheme - f.) If you're having trouble getting this script to run, remember you need to install the MySQL development headers/libraries as well as the standard installation. - g.) Make sure your user account has privileges to view and modify the ModelDB scheme. - h.) Should run with no errors. - i.) Download the default database content from here: - http://bioseed.mcs.anl.gov/~chenry/sql.tgz - j.) Extract the SQL file, and import it into the "ModelDB" scheme created in step 3.e -4.) Set up MySQL database backend - a.) Download sqllite file http://bioseed.mcs.anl.gov/~devoid/ModelDB-sqlite.tgz - b.) Extract to the Model-SEED-core/data/ directory - c.) Load SQL-lite database from file: - sqlite3 Model-SEED-core/data/ModelDB/ModelDB.db < Model-SEED-core/data/ModelDB/ModelDB.sqlite; - d.) Delete the ModelDB.sqlite file - e.) Run this command: Model-SEED-core/bin/ms-config load "Name of your config file that you filled out in steps 2.b and 4.b" -5.) Test the Model SEED - a.) Run this command: Model-SEED-core/bin/ModelDriver \ No newline at end of file +See instructions at: +http://bionet.mcs.anl.gov/index.php/Configuring_the_Model_SEED_Distribution \ No newline at end of file diff --git a/Linux and OSX Installation Instructions.txt b/Linux and OSX Installation Instructions.txt index 5ec3937..5c984bd 100644 --- a/Linux and OSX Installation Instructions.txt +++ b/Linux and OSX Installation Instructions.txt @@ -1,13 +1,3 @@ -1.) Make sure that git is installed on your computer -2.) Ensure that the following perl libraries are installed - a.) File/Copy/Recursive - b.) Spreadsheet/WriteExcel - c.) XML/DOM - d.) YAML - e.) DBD/mysql -3.) Run the following commands in bash to download and install the Model SEED: -curl https://raw.github.com/ModelSEED/Model-SEED-core/master/lib/ModelSEED/ModelSEEDScripts/bootstrap.sh > bootstrap.sh -chmod +x bootstrap.sh -./bootstrap.sh "path to location where Model SEED should be installed" -4.) Open the file, "Configuration Instructions" located in the ModelSEED installation directory, and follow these instructions +See instructions at: +http://bionet.mcs.anl.gov/index.php/Installing_the_Model_SEED_Distribution