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Commits (1)
### About
## About
This project contains the different software layers of the Gesall big data platform for genome data analysis.
......@@ -7,10 +7,16 @@ 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.
### Automated Building
Note the path of the base directory where the gesall-core, gesall-htsjdk, gesall-picard and gesall-libs is present.
## Automated Building
Before starting make a note the path of the base directory where the gesall-core, gesall-htsjdk, gesall-picard and gesall-libs is present.
#### Update build.xml files
#### Pre-requisites
To build the gesall-core code base, these things needs to be ensured first.
1. gesall-htsjdk, gesall-picard, gesall-libs folders are present parallel to gesall-core
2. gesall-htsjdk and gesall-picard needs to have been built first! The build process picks up jar files from the dist/ directory of these two modules.
3. Make sure your JAVA_HOME environment variables are setup, so as to use standard java commands (eg: jar, ant etc.)
#### Update hadoop home dir in the build.xml files
In the ant-build/ folder we need to update the path of the haddop home directory if we are building from scratch.
Update the value of the variable `hadoophome` in `build_clean.xml` and `build_md.xml`
......@@ -21,12 +27,6 @@ After going into the gesall-core dir simply run 'build.sh' with this path:
$> bash ./build.sh -dir=<path-to-your-base-dir>
```
#### Pre-requisites
To build the gesall-core code base, these things needs to be ensured first.
1. gesall-htsjdk, gesall-picard, gesall-libs folders are present parallel to gesall-core
2. gesall-htsjdk and gesall-picard needs to have been built first! The build process picks up jar files from the dist/ directory of these two modules.
3. Make sure your JAVA_HOME environment variables are setup, so as to use standard java commands (eg: jar, ant etc.)
#### 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_md.xml, to build Runnable jar files for the program.clean.latest and program.md.latest module respectively.
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