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Describe how GATK finds walkers. Change the example to avoid copying the class file into the walkers directory. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@104 348d0f76-0448-11de-a6fe-93d51630548a
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hanna 2009-03-19 22:41:12 +00:00
parent 104e2811ec
commit 6fdd622160
2 changed files with 17 additions and 2 deletions
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doc/GATK_Hello_World.tex
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@ -27,7 +27,7 @@ Download and build the source as follows:
\section{Getting Started} \section{Getting Started}
The core concept behind GATK is the walker, a class that implements the The core concept behind GATK is the walker, a class that implements the
three core operations, filtering, mapping, and reducing. three core operations: filtering, mapping, and reducing.
\begin{description} \begin{description}
\item [filter] reduces the size of the dataset by applying a predicate. \item [filter] reduces the size of the dataset by applying a predicate.
@ -41,11 +41,26 @@ Users of the GATK will provide a walker to run their analyses. The engine
will produce a result by first filtering the dataset, running a map operation, will produce a result by first filtering the dataset, running a map operation,
and finally reducing the map operation to a single result. and finally reducing the map operation to a single result.
\section{Creating a Walker}
To be loaded by GATK, the walker must satisfy the following properties:
\begin{enumerate}
\item It must be a loose class, not packaged into a jar file.
\item It must be in the unnamed package (in other words, the source
should not start with a package declaration).
\item It must subclass one of the basic walkers in the
org.broadinstitute.sting.gatk.walkers package: BasicReadWalker or
BasicLociWalker.
\item It must live in the directory \$STING\_HOME/dist/walkers.
\end{enumerate}
\section{Example} \section{Example}
This walker will print output for each read it sees, eventually computing the This walker will print output for each read it sees, eventually computing the
total number of reads by mapping every read to 1 and summing all the 1s to total number of reads by mapping every read to 1 and summing all the 1s to
realize the total number of reads. realize the total number of reads.
\begin{samepage}
Copy the following text into the file \$STING\_HOME/dist/walkers/HelloWalker.java:
\begin{verbatim} \begin{verbatim}
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
@ -74,6 +89,7 @@ public class HelloWalker extends BasicReadWalker<Integer,Long> {
} }
} }
\end{verbatim} \end{verbatim}
\end{samepage}
To compile the walker: To compile the walker:
\begin{verbatim} \begin{verbatim}
setenv CLASSPATH $STING_HOME/dist/GenomeAnalysisTK.jar:$STING_HOME/dist/sam-1.0.jar setenv CLASSPATH $STING_HOME/dist/GenomeAnalysisTK.jar:$STING_HOME/dist/sam-1.0.jar
@ -82,7 +98,6 @@ javac HelloWalker.java
To run the walker: To run the walker:
\begin{verbatim} \begin{verbatim}
mkdir $STING_HOME/dist/walkers mkdir $STING_HOME/dist/walkers
cp HelloWalker.java $STING_HOME/dist/walkers
java -Xmx4096m -jar dist/GenomeAnalysisTK.jar \ java -Xmx4096m -jar dist/GenomeAnalysisTK.jar \
INPUT_FILE=/broad/1KG/legacy_data/trio/na12878.bam \ INPUT_FILE=/broad/1KG/legacy_data/trio/na12878.bam \
ANALYSIS_NAME=Hello L=chr1:10000000-10000100 ANALYSIS_NAME=Hello L=chr1:10000000-10000100