Author: mes
Date: 2010-08-02 17:31:15 -0700 (Mon, 02 Aug 2010)
New Revision: 21125
Modified:
cytoscape/trunk/README.txt
Log:
updated readme
Modified: cytoscape/trunk/README.txt
===================================================================
--- cytoscape/trunk/README.txt 2010-08-03 00:22:02 UTC (rev 21124)
+++ cytoscape/trunk/README.txt 2010-08-03 00:31:15 UTC (rev 21125)
@@ -17,32 +17,15 @@
Cytoscape now contains the following directory structure:
-
cytoscape
+
- +---resources/ Contains various files used to compile or run cytoscape,
- + e.g. shell scripts, annotation files, props files etc.
+ +---application/ This directoy contains a maven project that builds and
+ + assembles the Cytoscape application jar.
+
- +---build/ This directoy is automatically generated by Ant. After
compilation,
- + this directory will contain all generated class files.
- +
- +---images/ Contains image files.
- +
- +---lib/ Contains all JAR files.
- +
- +---src/ Contains all source .java files.
- +
- +---testData/ Contains all test and sample data.
- +
- +---tools/ Contains misc. tools for cytoscape distribution.
- +
- +---docs/ Contains all user documentation and manuals.
- +
- +---plugins/ Contains all core plugins.
- +
- +---licences/ Contains all third party licenses.
- +
- +---help/ Contains all javahelp files and images.
+ +---distribution/ Contains a maven project that assembles the Cytoscape
+ distribution based on the core plugins and the jar file
+ built by application. This directory includes all shell
+ scripts, sample data, and licenses for the distribution.
III. New Build Process
@@ -50,166 +33,36 @@
To build cytoscape:
-1. Download and install Jakarta Ant. Download from: http://ant.apache.org/.
-Installation instructions are available at:
http://ant.apache.org/manual/install.html.
+1. Download and install Apache Maven: http://maven.apache.org/
-2. To compile cytoscape, type:
+2. To compile the Cytoscape:
+ a. go into the application directory:
- ant all
+ cd application
-3. To run cytoscape, type:
+ b. execute maven:
- ant run
+ mvn install
-If cytoscape appears, everything is set up correctly!
+3. To run cytoscape:
+ a. go into the distribution directory:
-For questions, email Mike Smoot: [email protected]
+ cd distribution
+ b. build the maven assembly:
-IV. Doing a Full Cytoscape Release
-===================================
+ mvn assembly:assembly
-This section contains notes / tasks for doing a full Cytoscape release. Doing
a full release
-of Cytoscape is rather involved. Some of the tasks are automated and some are
manual.
+ c. go into the target directory:
- Core Release Tasks
- -------------------
- Setup.
- Depending on whether you're creating a release from the trunk
or from
- a release branch you should do fresh checkouts of cytoscape,
corelibs,
- and core plugins
+ cd target/asdf/asdf
- mkdir release
- cd release
- svn co
svn+ssh://grenache.ucsd.edu/cellar/common/svn/cytoscape/trunk cytoscape
- svn co
svn+ssh://grenache.ucsd.edu/cellar/common/svn/corelibs/trunk corelibs
- svn co
svn+ssh://grenache.ucsd.edu/cellar/common/svn/coreplugins/trunk coreplugins
+ d. This will include the basic Cytoscape distribution.
- Compile the core libraries and copy jars to the cytoscape dir.
- cd corelibs
- ant all
- cp build/*.jar ../cytoscape/lib/.
+For questions, email Mike Smoot: [email protected]
- Compile Cytoscape with new libraries. This creates the cytoscape.jar
file
- needed by coreplugins to compile.
- cd ../cytoscape
- ant all
-
- Compile core plugins with new cytoscape.jar and copy jars to cytoscape
- dir.
-
- cd ../coreplugins
- ant all
- cp build/*.jar ../cytoscape/plugins/core/.
-
- Modify the Cytoscape Version Number in build.xml
- The ant build.xml file contains a property that looks like this:
-
- <property name="version.num" value="2.6.0"/>
-
- Note that the version.num property can't contain any alphabetic
- characters. If you want to create a beta release, append text
to
- the "version" property like so:
-
- <property name="version" value="${version.num}-beta1"/>
-
- Ensure that the Cytoscape Manual is up-to-date. See the
- DOC_GENERATION_README.txt file in the "docs" subdir for details.
- The manual really only needs to be updated for major releases and is
more than a
- little bit of a hassle.
-
- Recompile cytoscape.
-
- ant clean all
-
- Once cytoscape compiles cleanly with the new corelibs, coreplugins, and
- possibly updated documentation, TEST the thing!!! At a minimum start
- cytoscape and load a session file and play around with a network.
-
- Ok, so now you've got cytoscape compiling and running with the latest
- coreplugins and corelibs, so commit the new plugins and libs:
-
- cd cytoscape
- svn commit -m "commiting new libs and plugins for release 2.x"
-
- Now tag the cytoscape, coreplugins, and corelibs releases. It is
important
- that coreplugins and corelibs get tagged at the same time as cytoscape
so
- that these releases can be recreated in the future. The tag convention
we
- have adopted looks like this: "Cyto-2.5.2". Please follow this
convention.
-
- To tag the release:
-
- svn copy \
-
svn+ssh://grenache.ucsd.edu/cellar/common/svn/cytoscape/branches/cy-release-branch-x
\
-
svn+ssh://grenache.ucsd.edu/cellar/common/svn/cytoscape/tags/cyto_version
-
- svn copy \
-
svn+ssh://grenache.ucsd.edu/cellar/common/svn/coreplugins/branches/cy-release-branch-x
\
-
svn+ssh://grenache.ucsd.edu/cellar/common/svn/coreplugins/tags/cyto_version
-
- svn copy \
-
svn+ssh://grenache.ucsd.edu/cellar/common/svn/corelibs/branches/cy-release-branch-x
\
-
svn+ssh://grenache.ucsd.edu/cellar/common/svn/corelibs/tags/cyto_version
-
- Create the final release files
- To do so, run:
-
- ant clean dist
-
- The final release files are all placed in cytoscape/build/dist,
- including the Javadoc API files.
-
- NOTE: The installation bundles are created using install4j. You
- will need install4j installed on your machine and you must
- have the environment variable INSTALL4J_HOME set and pointing
- to the location of the install4j install.
-
- Deploy the new release files.
- Copy all files to their release directory on the distribution
- server. Currently this is chianti.ucsd.edu and each release
- lives in a subdirectory of /var/www/html.
-
- The subdirectory *MUST* be named correctly for PHP on the
website to
- work, like:
-
- Cyto-2_5_2
- or
- Cyto-2_6-beta
-
-
- Update Cytocape.org Web Site
- ----------------------------
-
- svn co file:///cellar/common/svn/cyto_web/trunk cyto_web
-
- Make sure the Cytoscape Manual (PDF) is Up-to-Date
- We currently keep a copy of CytoscapeX_YManual.pdf checked into
- two places: cytscape/user_docs and cyto_web/manual.
cytoscape/user_docs is
- the definitive one, and cyto_web/manual is the copy.
-
- Before doing a full release, make sure to copy the latest
manual from
- cytoscape/user_docs to cyto_web/manual, and check in the latest
version.
-
- Update cyto_web/config.php
-
- This file contains global configurations for cytoscape.org
- You will need to add variable links for the newly released
- version of Cytoscape.
-
- Update cyto_web/index.php with an announcement for the new release. See
- what we've done for past releases. Major release should list the major
- new features and minor releases should have smaller announcements.
-
- Deploy Everything to cytoscape.org
- To do so, update cyto_web/cyto.properties with a valid
user/password (If you don't
- have one, email Mike) Then, type:
-
- ant deploy
-
-
- Tell the world!
- ----------------------------
- Send an email announcement to the cytoscape-discuss and
cytoscape-announce
- mailing lists. Include a link to the new release downloads.
+IV. Doing a Full Cytoscape Release
+===================================
+???
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