diff --git a/public/java/test/org/broadinstitute/sting/BaseTest.java b/public/java/test/org/broadinstitute/sting/BaseTest.java
index 07f46c1c3..61bb8b34b 100755
--- a/public/java/test/org/broadinstitute/sting/BaseTest.java
+++ b/public/java/test/org/broadinstitute/sting/BaseTest.java
@@ -83,7 +83,7 @@ public abstract class BaseTest {
      */
     public static final String MD5_FILE_DB_SUBDIR = "integrationtests";
 
-    public static final String testDir = "testdata/";
+    public static final String testDir = "public/testdata/";
 
     /** before the class starts up */
     static {
diff --git a/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java
index a17c162f5..1e4625bf0 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java
@@ -60,8 +60,8 @@ public class GenomeAnalysisEngineUnitTest extends BaseTest {
         GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();
 
         Collection<SAMReaderID> samFiles = new ArrayList<SAMReaderID>();
-        samFiles.add(new SAMReaderID(new File("testdata/exampleBAM.bam"), new Tags()));
-        samFiles.add(new SAMReaderID(new File("testdata/exampleBAM.bam"), new Tags()));
+        samFiles.add(new SAMReaderID(new File("public/testdata/exampleBAM.bam"), new Tags()));
+        samFiles.add(new SAMReaderID(new File("public/testdata/exampleBAM.bam"), new Tags()));
 
         testEngine.setSAMFileIDs(samFiles);
         testEngine.checkForDuplicateSamFiles();
@@ -72,10 +72,10 @@ public class GenomeAnalysisEngineUnitTest extends BaseTest {
         GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();
 
         Collection<SAMReaderID> samFiles = new ArrayList<SAMReaderID>();
-        samFiles.add(new SAMReaderID(new File("testdata/exampleBAM.bam"),  new Tags()));
-        samFiles.add(new SAMReaderID(new File("testdata/exampleNORG.bam"), new Tags()));
-        samFiles.add(new SAMReaderID(new File("testdata/exampleBAM.bam"),  new Tags()));
-        samFiles.add(new SAMReaderID(new File("testdata/exampleNORG.bam"), new Tags()));
+        samFiles.add(new SAMReaderID(new File("public/testdata/exampleBAM.bam"),  new Tags()));
+        samFiles.add(new SAMReaderID(new File("public/testdata/exampleNORG.bam"), new Tags()));
+        samFiles.add(new SAMReaderID(new File("public/testdata/exampleBAM.bam"),  new Tags()));
+        samFiles.add(new SAMReaderID(new File("public/testdata/exampleNORG.bam"), new Tags()));
 
         testEngine.setSAMFileIDs(samFiles);
         testEngine.checkForDuplicateSamFiles();
@@ -97,7 +97,7 @@ public class GenomeAnalysisEngineUnitTest extends BaseTest {
         GATKArgumentCollection argCollection = new GATKArgumentCollection();
         testEngine.setArguments(argCollection);
 
-        File fastaFile = new File("testdata/exampleFASTA.fasta");
+        File fastaFile = new File("public/testdata/exampleFASTA.fasta");
         GenomeLocParser genomeLocParser = new GenomeLocParser(new IndexedFastaSequenceFile(fastaFile));
         testEngine.setGenomeLocParser(genomeLocParser);
 
diff --git a/public/java/test/org/broadinstitute/sting/utils/bed/BedParserUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/bed/BedParserUnitTest.java
index e592c99b9..56bf66f53 100644
--- a/public/java/test/org/broadinstitute/sting/utils/bed/BedParserUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/bed/BedParserUnitTest.java
@@ -21,7 +21,7 @@ public class BedParserUnitTest extends BaseTest {
 
     private static IndexedFastaSequenceFile seq;
     private GenomeLocParser genomeLocParser;
-    private File bedFile = new File("testdata/sampleBedFile.bed");
+    private File bedFile = new File("public/testdata/sampleBedFile.bed");
 
     @BeforeClass
     public void beforeTests() {
diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java
index 2e618d5eb..e912f97e9 100644
--- a/public/java/test/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java
@@ -39,7 +39,7 @@ import java.io.IOException;
  */
 public class HapMapUnitTest {
     // our sample hapmap file
-    private final static File hapMapFile = new File("testdata/genotypes_chr1_ASW_phase3.3_first500.hapmap");
+    private final static File hapMapFile = new File("public/testdata/genotypes_chr1_ASW_phase3.3_first500.hapmap");
     private final static String knownLine = "rs2185539 C/T chr1 556738 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_r" +
             "s2185539:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC TC TT CT CC CC CC CC CC CC CC CC CC";
     /**
diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java
index 3929ff388..2f6b589f4 100755
--- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java
@@ -17,8 +17,8 @@ import java.util.*;
  */
 public class IndexFactoryUnitTest {
 
-    File inputFile = new File("testdata/HiSeq.10000.vcf");
-    File outputFile = new File("testdata/onTheFlyOutputTest.vcf");
+    File inputFile = new File("public/testdata/HiSeq.10000.vcf");
+    File outputFile = new File("public/testdata/onTheFlyOutputTest.vcf");
     File outputFileIndex = Tribble.indexFile(outputFile);
 
     /**
diff --git a/public/java/test/org/broadinstitute/sting/utils/text/ListFileUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/text/ListFileUtilsUnitTest.java
index f85a2f599..f0b1de6fe 100644
--- a/public/java/test/org/broadinstitute/sting/utils/text/ListFileUtilsUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/text/ListFileUtilsUnitTest.java
@@ -49,12 +49,12 @@ public class ListFileUtilsUnitTest extends BaseTest {
     public void testIgnoreBlankLinesInBAMListFiles() throws Exception {
         File tempListFile = createTempListFile("testIgnoreBlankLines",
                                                "",
-                                               "testdata/exampleBAM.bam",
+                                               "public/testdata/exampleBAM.bam",
                                                "         "
                                               );
 
         List<SAMReaderID> expectedBAMFileListAfterUnpacking = new ArrayList<SAMReaderID>();
-        expectedBAMFileListAfterUnpacking.add(new SAMReaderID(new File("testdata/exampleBAM.bam"), new Tags()));
+        expectedBAMFileListAfterUnpacking.add(new SAMReaderID(new File("public/testdata/exampleBAM.bam"), new Tags()));
 
         performBAMListFileUnpackingTest(tempListFile, expectedBAMFileListAfterUnpacking);
     }
@@ -63,13 +63,13 @@ public class ListFileUtilsUnitTest extends BaseTest {
     public void testCommentSupportInBAMListFiles() throws Exception {
         File tempListFile = createTempListFile("testCommentSupport",
                                                "#",
-                                               "testdata/exampleBAM.bam",
-                                               "#testdata/foo.bam",
-                                               "      # testdata/bar.bam"
+                                               "public/testdata/exampleBAM.bam",
+                                               "#public/testdata/foo.bam",
+                                               "      # public/testdata/bar.bam"
                                               );
 
         List<SAMReaderID> expectedBAMFileListAfterUnpacking = new ArrayList<SAMReaderID>();
-        expectedBAMFileListAfterUnpacking.add(new SAMReaderID(new File("testdata/exampleBAM.bam"), new Tags()));
+        expectedBAMFileListAfterUnpacking.add(new SAMReaderID(new File("public/testdata/exampleBAM.bam"), new Tags()));
 
         performBAMListFileUnpackingTest(tempListFile, expectedBAMFileListAfterUnpacking);
     }
diff --git a/public/java/test/org/broadinstitute/sting/utils/threading/GenomeLocProcessingTrackerUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/threading/GenomeLocProcessingTrackerUnitTest.java
index df4e1660d..78ab916db 100644
--- a/public/java/test/org/broadinstitute/sting/utils/threading/GenomeLocProcessingTrackerUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/threading/GenomeLocProcessingTrackerUnitTest.java
@@ -29,7 +29,7 @@ public class GenomeLocProcessingTrackerUnitTest extends BaseTest {
     IndexedFastaSequenceFile fasta = null;
     GenomeLocParser genomeLocParser = null;
     String chr1 = null;
-    private final static String FILE_ROOT = "testdata/GLPTFile";
+    private final static String FILE_ROOT = "public/testdata/GLPTFile";
 
     @BeforeTest
     public void before() {