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[ADAM-335] Updated README.md to reflect migration to appassembler. #337

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[ADAM-335] Updated README.md to reflect migration to appassembler. #337

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24 changes: 16 additions & 8 deletions README.md
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Expand Up @@ -76,18 +76,19 @@ reads and pileups, run flagstat, etc. We use this script to test that ADAM is wo

## Running ADAM

The ADAM jar file is a self-executing jar file with all dependencies included.
ADAM is packaged via [appassembler](http://mojo.codehaus.org/appassembler/appassembler-maven-plugin/) and includes all necessary
dependencies

You might want to add the following to your `.bashrc` to make running `adam` easier:

```
adam_jar="/workspace/adam/adam-cli/target/adam-0.6.0-SNAPSHOT.jar"
alias adam="java -Xmx4g -jar $adam_jar"
alias adam=". $ADAM_HOME/adam-cli/target/appassembler/bin/adam"
```

Of course, you will want to change the `adam_jar` variable to point to the directory
you placed ADAM on your local filesystem. You can also modify `-Xmx4g` to either give
ADAM more or less memory depending on your system.
`$ADAM_HOME` should be the path to where you have checked ADAM out on your local filesystem.
To change any Java options (e.g., the memory settings --> "-Xmx4g", or to pass Java properties)
set the `$JAVA_OPTS` environment variable. Additional details about customizing the appassembler
runtime can be found [here](http://mojo.codehaus.org/appassembler/appassembler-maven-plugin/usage-script.html).

Once this alias is in place, you can run adam by simply typing `adam` at the commandline, e.g.

Expand Down Expand Up @@ -119,7 +120,7 @@ Choose one of the following commands:
```

ADAM outputs all the commands that are available for you to run. To get
help for a specific command, run `adam <command> -h`, e.g.
help for a specific command, run `adam <command>` without any additional arguments.

````
$ adam transform --help
Expand Down Expand Up @@ -171,12 +172,19 @@ $ adam flagstat NA12878_chr20.adam
````

In practice, you'll find that the ADAM `flagstat` command takes orders of magnitude less
time than samtools to compute these statistics. For example, on my MacBook Pro the command
time than samtools to compute these statistics. For example, on a MacBook Pro the command
above took 17 seconds to run while `samtools flagstat NA12878_chr20.bam` took 55 secs.
On larger files, the difference in speed is even more dramatic. ADAM is faster because
it's multi-threaded and distributed and uses a columnar storage format (with a projected
schema that only materializes the read flags instead of the whole read).

## Running Plugins

ADAM allows users to create plugins via the [ADAMPlugin](https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/scala/org/bdgenomics/adam/plugins/ADAMPlugin.scala)
trait. These plugins are then imported using the Java classpath at runtime. To add to the classpath when
using appassembler, use the `$CLASSPATH_PREFIX` environment variable. For an example of how to use
the plugin interface, please see the [adam-plugins repo](https://github.com/heuermh/adam-plugins).

# Getting In Touch

## Mailing List
Expand Down