migration to mvn along with GATK 3.1's new build process

README.md

@@ -24,12 +24,20 @@ BUILD STEPS
 
     # get MuTect source
     git clone git@github.com:broadinstitute/mutect.git
-    cd ..
 
     # get the GATK source and set to the latest tested version
     git clone git@github.com:broadgsa/gatk-protected.git
     cd gatk-protected
-    git reset --hard 2.7-1-g42d771f
+    git reset --hard 3.1 
 
-    # build
-    ant -Dexternal.dir=`pwd`/../mutect-src -Dexecutable=mutect package
+    # build the GATK first and install it to the local mvn repo.  Once GATK publishes to a public repo this will be much simpler
+    mvn -Ddisable.queue install
+
+	# build MuTect and run unit tests (the target jar will be in target/mutect-*.jar)
+	cd ../mutect
+	mvn verify
+
+	# run integration tests, if you like
+	./run_regression.pl
+	./tieout_regression.pl
+

make_mutect_release.pl

@@ -8,7 +8,6 @@
 
 my $BASE_DIR = "$TMP_DIR/mutect-dist";
 my $GATK_DIR = "$BASE_DIR/gatk-protected";
-my $MUTECT_DIR = "$BASE_DIR/mutect-src";
 my $cwd = `pwd`;
 chomp($cwd);
 
@@ -21,10 +20,10 @@
 
 
 # update CGA and get revision info
-system("cd $MUTECT_DIR && git clone git\@github.com:broadinstitute/mutect.git") == 0 or die();
+system("cd $BASE_DIR && git clone git\@github.com:broadinstitute/mutect.git") == 0 or die();
 
 # check to see if this tag exists
-my $cnt = `cd $MUTECT_DIR/mutect && git ls-remote --tags -q | grep refs/tags/$mutect_tag | wc -l`;
+my $cnt = `cd $BASE_DIR/mutect && git ls-remote --tags -q | grep refs/tags/$mutect_tag | wc -l`;
 chomp($cnt);
 if ($cnt == 0) { die("ERROR: release tag $mutect_tag does not exist!\n"); }
 system("cd $MUTECT_DIR/mutect && git reset --hard $mutect_tag") == 0 or die();
@@ -41,14 +40,14 @@
 `git describe --tags | awk '{ print "GATK Revision: " \$0 }' >> $TMP_DIST/version.txt`;
 
 # do a clean build
-system("cd $GATK_DIR && ant clean") == 0 or die();
-system("cd $GATK_DIR && ant -Dexternal.dir=$MUTECT_DIR -Dexecutable=mutect package") == 0 or die();
+system("cd $GATK_DIR && mvn -Ddisable.queue install") == 0 or die();
+system("cd $BASE_DIR/mutect && mvn verify") == 0 or die();
 
 # move the executable over to the release directory
-system("cp $GATK_DIR/dist/packages/muTect-*/muTect.jar $TMP_DIST/muTect-$mutect_tag.jar") == 0 or die();
+system("cp $BASE_DIR/mutect/target/mutect-*.jar $TMP_DIST/.") == 0 or die();
 
 # move the license over to the release directory
-system("cp $MUTECT_DIR/mutect/mutect.LICENSE.TXT $TMP_DIST/LICENSE.TXT") == 0 or die();
+system("cp $BASE_DIR/mutect/mutect.LICENSE.TXT $TMP_DIST/LICENSE.TXT") == 0 or die();
 
 # zip it up
 chdir($cwd);