[MOBY-guts] biomoby commit
Gary Schlitz
gss at pub.open-bio.org
Wed Jun 30 18:21:28 UTC 2004
gss
Wed Jun 30 14:21:28 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl
In directory pub.open-bio.org:/tmp/cvs-serv30997/S-MOBY/ref-impl
Modified Files:
INSTALL.html
Log Message:
Fixed installation instructions to reflect problems that Ardavan K found.
moby-live/S-MOBY/ref-impl INSTALL.html,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/INSTALL.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/INSTALL.html 2004/06/10 23:10:44 1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/INSTALL.html 2004/06/30 18:21:28 1.2
@@ -1,13 +1,14 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
+ <meta name="generator" content="HTML Tidy, see www.w3.org">
<title>Building and Installing Semantic MOBY</title>
</head>
<body>
<h2 style="text-align: center;">Building and Installing the Semantic
MOBY<br>
Reference Implementation</h2>
-<div style="text-align: justify;">This page contains step-by-step
+<div style="text-align: justify;"> This page contains step-by-step
instructions on building and installing the complete reference
implementation of Semantic MOBY. The complete installation includes a
reference implementation of a discovery/registration server
@@ -23,7 +24,7 @@
</div>
<br>
<h3>Prerequisites</h3>
-<div style="text-align: justify;">Before beginning to build the
+<div style="text-align: justify;"> Before beginning to build the
reference implementation, certain software must be installed on the
machine that is to host the installation. In the following list, the
recommended software versions are the only ones that the author has
@@ -39,19 +40,15 @@
<br>
</li>
<li>
- <div style="text-align: justify;"><a href="http://ant.apache.org">Apache
+ <div style="text-align: justify;"> <a href="http://ant.apache.org">Apache
Ant</a> (tested with version 1.6.1) should be installed and on the
-executable path. To check, type <code>'ant -version</code><code>' </code>(without
-the quotes) on a command line.<br>
- </div>
- <br>
- </li>
- <li style="text-align: justify;">One of the open source databases,
-either <a href="http://www.postgresql.org">PostgreSQL</a> (tested with
-version 7.4.1) or <a href="http://www.mysql.com">MySQL</a> (tested
-with version 4.0.18) should be installed and running, and a database
-named <code>smoby-dev</code> has been created.<br>
+executable path. To check, type <code>'ant -version</code><code>'</code>
+(without the quotes) on a command line.One of the open source
+databases, either <a href="http://www.postgresql.org">PostgreSQL</a>
+(tested with version 7.4.1) or <a href="http://www.mysql.com">MySQL</a>
+(tested with version 4.0.18) should be installed and running.<br>
<br>
+ </div>
</li>
<li style="text-align: justify;">The Semantic MOBY distribution has
been retrieved from CVS and saved locally. As of this writing, there
@@ -69,83 +66,108 @@
<h3>Installation steps</h3>
<ol type="1">
<li>
- <div style="text-align: justify;">Modify the <code>hosts</code>
+ <div style="text-align: justify;"> Modify the <code>hosts</code>
file of the computer that is to host the reference implementation, as
-described in the <code>for-hosts-file </code>file located in the <code>ref-impl/config-files/</code>
+described in the <code>for-hosts-file</code> file located in the <code>ref-impl/config-files/</code>
subdirectory of the reference implementation directory. Since one
computer is to host several example domains (s-moby.org, acmepubs.com,
etc.), this is the easiest way to make these virtual domain, hosted by
Apache Tomcat (see the next step) resolve to the local host.<br>
- </div>
<br>
+ </div>
</li>
<li>
- <div style="text-align: justify;">Install <a
+ <div style="text-align: justify;"> Install <a
href="http://jakarta.apache.org/tomcat">Apache Tomcat 5.0</a> (tested
with version 5.0.25) and start it. If all went well, you should be able
to open <a href="http://localhost:8080">http://localhost:8080</a> in a
browser. After making sure it is properly installed, shutdown Tomcat.<br>
+ <br>
</div>
+ </li>
+ <li>
+ <div style="text-align: justify;"> Modify Tomcat's main
+configuration file (<code>server.xml</code>), located in the <code>conf/</code>
+subdirectory of the Tomcat installation directory as instructed in the <code>for-tomcat-conf-server.xml</code>
+file, located in the <code>config-files/</code> subdirectory of the
+reference implementation directory. This modification sets up virtual
+hosts, accessible by name, that are all served by Tomcat 5.<br>
<br>
+ </div>
</li>
<li>
- <div style="text-align: justify;">Modify <tomcat-top-dir>Tomcat's
-main configuration file (<code>server.xml</code>), located in the <code>conf/</code>
-subdirectory of the Tomcat installation directory as instructed in the </tomcat-top-dir><code>for-tomcat-conf-server.xml
- </code>file, located in the <code>config-files/</code>
-subdirectory of the reference implementation directory. This
-modification sets up virtual hosts, accessible by name, that are all
-served by Tomcat 5.<br>
- </div>
- <tomcat-top-dir><br>
- </tomcat-top-dir></li>
- <li>
- <div style="text-align: justify;">Save a copy of the <ref-impl-top-dir><code>common.example.properties</code>
-file, located in the reference implementation<span
- style="font-family: monospace;"></span><code></code> directory, as <code>common.properties</code>
+ <div style="text-align: justify;"> Save a copy of the <code>common.example.properties</code>
+file, located in the reference implementation directory, as <code>common.properties</code>
(in the same directory). This file is used by the Ant build scripts,
and should be modified to reflect the system on which the reference
-implementation is being installed.</ref-impl-top-dir><br>
- <ref-impl-top-dir></ref-impl-top-dir></div>
- <ref-impl-top-dir><br>
- </ref-impl-top-dir></li>
- <li>
- <div style="text-align: justify;">From the command line, change
-directory to the reference implementation directory and <ref-impl-top-dir>run
- <code>'ant third-party' </code>(without the quotes). This
-retrieves third party components from CVS and builds them. Retrieving
-the components from CVS is admittedly less predictable than storing a
-version of the components with the Semantic MOBY distribution, but as
-the components (especially <a href="http://jena.sourceforge.net">Jena2</a>)
-are constantly being improved, it is considered more important to have
-the latest versions than to have stable versions. Currently, this step
-takes about three minutes on a 2GHz P4 machine with a broadband
-connection.</ref-impl-top-dir><br>
- <ref-impl-top-dir></ref-impl-top-dir></div>
- <br>
- <ref-impl-top-dir></ref-impl-top-dir></li>
- <li>
- <div style="text-align: justify;">From the command line, while
-still in the reference implementation directory, <ref-impl-top-dir>
-run '<code>ant deploy-to-tomcat</code>' (without the quotes). This
-compiles the Semantic MOBY reference implementation and deploys the
-various parts to run as Java Servlets under Tomcat 5.</ref-impl-top-dir><br>
- <ref-impl-top-dir></ref-impl-top-dir></div>
- <ref-impl-top-dir><br>
- </ref-impl-top-dir></li>
- <li>
- <div style="text-align: justify;">Copy the appropriate JDBC driver
-jar file into the <tomcat-top-dir><code>shared/lib</code>
-subdirectory of the Tomcat 5 installation. As of this writing, the
-latest PostgreSQL JDBC jar file
+implementation is being installed.<br>
+ <br>
+ </div>
+ </li>
+ <li>
+ <div style="text-align: justify;"> From the command line, change
+directory to the reference implementation directory and run <code>'ant
+third-party'</code> (without the quotes). This retrieves third party
+components from CVS and builds them. Retrieving the components from CVS
+is admittedly less predictable than storing a version of the components
+with the Semantic MOBY distribution, but as the components (especially <a
+ href="http://jena.sourceforge.net">Jena2</a>) are constantly being
+improved, it is considered more important to have the latest versions
+than to have stable versions. Currently, this step takes about three
+minutes on a 2GHz P4 machine with a broadband connection.<br>
+ <br>
+ </div>
+ </li>
+ <li>
+ <div style="text-align: justify;"> From the command line, while
+still in the reference implementation directory, run '<code>ant
+deploy-to-tomcat</code>' (without the quotes). This compiles the
+Semantic MOBY reference implementation and deploys the various parts to
+run as Java Servlets under Tomcat 5.<br>
+ <br>
+ </div>
+ </li>
+ <li>
+ <div style="text-align: justify;"> Copy the appropriate JDBC driver
+jar file into the <code>shared/lib</code> subdirectory of the Tomcat 5
+installation. As of this writing, the latest PostgreSQL JDBC jar file
was named <span style="font-style: italic;">postgresql.jar</span> and
-the latest MySQL driver was named <span style="font-style: italic;">mysql-connector-java-3.0.11-stable-bin.jar</span>.</tomcat-top-dir><br>
- <tomcat-top-dir></tomcat-top-dir></div>
- <tomcat-top-dir><br>
- </tomcat-top-dir></li>
+the latest MySQL driver was named <span style="font-style: italic;">mysql-connector-java-3.0.11-stable-bin.jar</span>.<br>
+ <br>
+ </div>
+ </li>
+ <li>
+ <div style="text-align: justify;"><!--StartFragment --> Using
+whatever tools are appropriate for your DBMS, create a database user
+(e.g. <code>joe</code>) with a password (e.g. <code>foobar</code>).
+For MySQL, the free MySQL Control Center works well, and for
+PostgreSQL, PGAdmin III works well.<br>
+ <br>
+ </div>
+ </li>
+ <li>
+ <div style="text-align: justify;"><!--StartFragment --> Create a
+database, and give it a name (e.g. <code>my-smoby-repository</code>).
+Make the owner of the database the user (e.g. <code>joe</code>)
+created in step 8.<br>
+ <br>
+ </div>
+ </li>
+ <li>
+ <div style="text-align: justify;"><!--StartFragment --> Modify <code>smoby.properties</code>,
+located in the <code>webapps/s-moby.org</code> subdirectory of the
+Tomcat installation directory, setting <code>DB_USER_ID</code> to the
+user (e.g. <code>joe</code>) created in step 8, <code>DB_PASSWORD</code>
+to the password (e.g. <code>foobar</code>) of the user created in step
+8, and <code>DB_REPOSITORY_NAME</code> to the database name (e.g. <code>my-smoby-repository</code>)
+used in step 8.Also modify <code>DB_URL</code> to include the name of
+the database used in step 9 (e.g. <code>jdbc:postgresql://localhost/my-smoby-repository</code>).<br>
+ <br>
+ </div>
+ </li>
<li>Start Tomcat. If all went well, you should be able to open <a
- href="http://www.s-moby.org:8080">http://www.s-moby.org:8080</a>
-in a browser. </li>
+ href="http://www.s-moby.org:8080">http://www.s-moby.org:8080</a> in a
+browser.</li>
</ol>
</body>
</html>
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