Commit 7ca2e415 authored by shubham mukherjee's avatar shubham mukherjee

update readme

parent e3303aea
......@@ -7,24 +7,33 @@ This project contains the different software layers of the Gesall big data platf
2. Data Partitioning schemes (with MapReduce wrappers) are in `program.{alignment|clean|md}.latest` packages.
3. Error Diagnosis programs are in `correctness.*` packages.
### Building
### Automated Building
Note the path of the base directory where the gesall-core / gesall-htsjdk / gesall-picard / gesall-libs is present.
After going into the gesall-core dir simply run 'build.sh' inserting the
##### Eclipse IDE
$> ./build.sh -dir=<path-to-your-base-dir>
#### What it does?
1. Replaces the path of your base directory in the Ant buils files to pickup the dependencies.
2. Uses ant_build/build_clean.xml and ant_build/build_clean.xml, to build Runnable jar files for the program.clean.latest and program.md.latest module respectively.
3. Package the program.alignment.latest into a jar file. Note that this is not directly runnable.
#### Output format
The directory out/ in the base directory contains the 3 jar files.
These can now be used with the Hadoop Infrastructure. Note that the jar doesn *not* contain any hadoop libraries itself.
### Building using Eclipse IDE
##### Import the code
1. Import the code from `gesall-core` repository into Eclipse.
2. Add `gesall-htsjdk` and `gesall-picard` Eclipse projects to dependencies in `Project->Properties->Java Build Path->Projects`.
3. Add all the external JAR files from `gesall-libs` into `Project->Properties->Java Build Path->Libraries`.
#### Exporting code as JAR files
##### Eclipse IDE
##### Building the jars
1. Use `File->Export->Runnable JAR` option with library handling set to `Extract required libraries into generated JAR`.
2. This will create a self-contained, fat JAR file.
3. Apache Hadoop JAR files in `gesall-libs` should be of the same version as the deployment Hadoop cluster.
##### Command line
1. There are some example `ant` build files in the `ant-build` directory.
2. These build files were generated using `Export->Ant buildfiles` option in Eclipse. But references to specific versions of Hadoop libraries were removed.
### License
Our code is released under MIT license.
\ No newline at end of file
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<project default="create_run_jar" name="Create Runnable Jar for Project gesall-core">
<!--this file was created by Eclipse Runnable JAR Export Wizard-->
<!--ANT 1.7 is required -->
<property name="homedir" value="/home/shubham/geneproject" />
<target name="create_run_jar">
<jar destfile="${homedir}/gesall-core/test1.jar" filesetmanifest="mergewithoutmain">
<manifest>
<!-- <attribute name="Main-Class" value="hdfs.clean.bam.bloom.md.MarkDuplicatesMain"/> -->
<attribute name="Main-Class" value="program.clean.latest.CleanMRMain"/>
<attribute name="Class-Path" value="."/>
</manifest>
<fileset excludes="picard_md_lib/*" dir="${homedir}/gesall-core/bin"/>
<zipfileset excludes="META-INF/*.SF" src="${homedir}/gesall-libs/apache/cmdline/commons-exec-1.2.jar"/>
<zipfileset excludes="META-INF/*.SF" src="${homedir}/gesall-libs/json/json-20140107.jar"/>
<zipfileset excludes="META-INF/*.SF" src="${homedir}/gesall-htsjdk/dist/snappy-java-1.0.3-rc3.jar"/>
<fileset dir="${homedir}/gesall-htsjdk/bin"/>
<zipfileset excludes="META-INF/*.SF" src="${homedir}/gesall-htsjdk/lib/testng/testng-5.5-jdk15.jar"/>
<zipfileset excludes="META-INF/*.SF" src="${homedir}/gesall-htsjdk/lib/commons-jexl-2.1.1.jar"/>
<zipfileset excludes="META-INF/*.SF" src="${homedir}/gesall-htsjdk/lib/snappy-java-1.0.3-rc3.jar"/>
<fileset dir="${homedir}/gesall-picard/bin"/>
<zipfileset excludes="META-INF/*.SF" src="${homedir}/gesall-picard/lib/testng/testng-5.5-jdk15.jar"/>
<zipfileset excludes="META-INF/*.SF" src="${homedir}/gesall-picard/lib/ant/bcel-5.2.jar"/>
<zipfileset excludes="META-INF/*.SF" src="${homedir}/gesall-libs/jopt/jopt-simple-4.8.jar"/>
<zipfileset excludes="META-INF/*.SF" src="${homedir}/gesall-libs/guava-18.0/guava-18.0.jar"/>
</jar>
</target>
</project>
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<project default="create_run_jar" name="Create Runnable Jar for Project gesall-core">
<!--this file was created by Eclipse Runnable JAR Export Wizard-->
<!--ANT 1.7 is required -->
<property name="homedir" value="/home/shubham/geneproject" />
<target name="create_run_jar">
<jar destfile="${homedir}/gesall-core/test1.jar" filesetmanifest="mergewithoutmain">
<manifest>
<!-- <attribute name="Main-Class" value="hdfs.clean.bam.bloom.md.MarkDuplicatesMain"/> -->
<attribute name="Main-Class" value="program.md.latest.MarkDuplicatesMain"/>
<attribute name="Class-Path" value="."/>
</manifest>
<fileset excludes="picard_md_lib/*" dir="${homedir}/gesall-core/bin"/>
<zipfileset excludes="META-INF/*.SF" src="${homedir}/gesall-libs/apache/cmdline/commons-exec-1.2.jar"/>
<zipfileset excludes="META-INF/*.SF" src="${homedir}/gesall-libs/json/json-20140107.jar"/>
<zipfileset excludes="META-INF/*.SF" src="${homedir}/gesall-htsjdk/dist/snappy-java-1.0.3-rc3.jar"/>
<fileset dir="${homedir}/gesall-htsjdk/bin"/>
<zipfileset excludes="META-INF/*.SF" src="${homedir}/gesall-htsjdk/lib/testng/testng-5.5-jdk15.jar"/>
<zipfileset excludes="META-INF/*.SF" src="${homedir}/gesall-htsjdk/lib/commons-jexl-2.1.1.jar"/>
<zipfileset excludes="META-INF/*.SF" src="${homedir}/gesall-htsjdk/lib/snappy-java-1.0.3-rc3.jar"/>
<fileset dir="${homedir}/gesall-picard/bin"/>
<zipfileset excludes="META-INF/*.SF" src="${homedir}/gesall-picard/lib/testng/testng-5.5-jdk15.jar"/>
<zipfileset excludes="META-INF/*.SF" src="${homedir}/gesall-picard/lib/ant/bcel-5.2.jar"/>
<zipfileset excludes="META-INF/*.SF" src="${homedir}/gesall-libs/jopt/jopt-simple-4.8.jar"/>
<zipfileset excludes="META-INF/*.SF" src="${homedir}/gesall-libs/guava-18.0/guava-18.0.jar"/>
</jar>
</target>
</project>
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