[MOBY-guts] biomoby commit

[senger at ebi.ac.uk]

senger
Thu Sep 25 08:22:06 EDT 2003
Update of /home/repository/moby/moby-live/Java
In directory pub.open-bio.org:/tmp/cvs-serv19535

Modified Files:
	README 
Log Message:


moby-live/Java README,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Java/README,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/README	2003/09/24 14:38:28	1.5
+++ /home/repository/moby/moby-live/Java/README	2003/09/25 12:22:06	1.6
@@ -1,73 +1,85 @@
-# !!!! work in progress !!!!
-# wait... (will be back on 25th September 2003)
-#
-#  You *can* use this script to compile everything anytime,
-#  but you *must* use it the first time (because it gathers
-#  all third-party libraries needed for compilation).
-#  Otherwise you *may* use build-dev.sh which is slightly
-#  faster because it does not attemp to fetch libraries.
-#
-#  $Id$
-
-# --- setup environment
-#
-#  This script can make use of the following environment variables:
-#
-#     ANT_HOME ... pointing to a directory with Ant libraries.
-#              Default (used if variable is not set): ./lib/ant/
-#     JAVA_HOME ... pointing to a directory with your Java JDK.
-#              If not set the script tries to find it anyway.
-#     USE_JIKES ... saying what Java compiler to use:
-#              USE_JIKES=1  => jikes is used (it is up to you to
-#                              make sure that an executable 'jikes'
-#                              is on your PATH)
-#              Default: USE_JIKES is unset (therefore, no jikes used).
-
-
-
-
 This directory (and its subdirectories) contains Java clients
 accessing Moby registry, and, hopefully in the future, more
 implementation of pure Java in BioMoby project.
 
 Find more in docs/index.html.
 
-HOW TO USE IT
--------------
+If you do not want to build it you can use the binary distribution
+which is available at http://industry.ebi.ac.uk/~senger/jMoby/dist/.
 
-Set your Java environment as shown in setenv.csh.template or
-setenv.sh.template. Then you can start the testing client by typing:
+HOW TO BUILD IT
+---------------
 
-   java TestingCentral
+Just type:
+   ./build.sh
+or, on Windows platform.
+   build.bat
+
+You *can* use 'build.sh' (or 'build.bat') script to compile everything
+anytime, but you *must* use it the first time (because it gathers all
+third-party libraries needed for compilation).  Otherwise you *may*
+use 'build-dev.sh' (or 'build-dev.bat') which is slightly faster
+because it does not attemp to fetch libraries.
+
+Therefore, when re-building, you would normally type:
+   ./build-dev.sh
+or, on Windows platform.
+   build-dev.bat
+
+In order to find what tasks are available, type:
+
+   ./build-dev.sh -projecthelp
+or
+   build-dev.bat -projecthelp
+
+The available task can be specified on the command line of the
+building scripts. For example:
+   ./build-dev.sh all
+Default task is 'compile'.
+
+The building scripts can make use of the following environment
+variables:
+
+   ANT_HOME
+      Pointing to a directory with Ant libraries.
+      Default (used if variable is not set): ./lib/ant/.
+      Note that you *do not* need to have Ant install - it comes with
+      the CVS module.
+
+   JAVA_HOME
+      Pointing to a directory with your Java JDK.
+      If not set the script tries to find it anyway (but not for the
+      Windows platform - I do not know how to do it there :-)).
+
+   USE_JIKES
+      Saying what Java compiler to use:
+      USE_JIKES=1  => jikes is used (it is up to you to
+                      make sure that an executable 'jikes'
+                      is on your PATH)
+      Default: USE_JIKES is unset (therefore, no jikes used).
 
-or a more flexible command-line client by typing:
+Last note for developers:
+   If you want to commit your changes back consider to copy file(s)
+'.cvsignore.template' into '.cvsignore. This will save you from
+warning message about local files which you do not want to commit
+(e.g. generated 'build' directory).
 
-   java MobyCmdLineClient -help
 
-You need to have Apache Axis, Java Servlet API and XLM-parsing
-classes. One place to look for them is http://xml.apache.org/axis.
+HOW TO USE IT
+-------------
 
+After building it all, invoke available clients using provided (and
+very simple) scripts:
 
-HOW TO BUILD IT
----------------
+   ./run-cmdline-client -help
+   ./run-testing-central
 
-Note on building:
-   At the moment there is a Makefile to compile all Java classes and
-to generate an API documentation for some of them. I would rather see
-this done by Ant - I would appreciate if anybody can add here a
-'build.xml' file and convert the whole building process under
-Ant. Thanks!
-
-Having set the Java environment as described above type one of these:
-   make
-   make clean
-   make doc
+or, on Windows platforms:
 
-Notes for developers:
-   If you want to commit your changes back consider to copy file(s)
-'.cvsignore.template' into '.cvsignore. This will save you from
-warning message about local files which you do not want to commit
-(e.g. setenv.sh).
+   run-cmdline-client.bat -help
+   run-testing-central.bat
+
+Enjoy it!
 
 --------------------------------------------------------------------
 Comments to the biomoby mailing lists, or directly to Martin Senger