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Merge pull request #673 from broadinstitute/ks_md5_db_per_test_run 

Creating and MD5DB per each test, instead of overwriting in the top dir
This commit is contained in:
droazen 2014-07-08 10:58:59 -04:00
parent f084fa5ab2 2129aa05d8
commit b2e51838d7
4 changed files with 7 additions and 2 deletions
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1
public/gatk-engine/pom.xml
View File

@ -15,6 +15,7 @@
<properties>
<gatk.basedir>${project.basedir}/../..</gatk.basedir>
<gatk.packagetests.artifactId>gatk-package-distribution</gatk.packagetests.artifactId>
</properties>
<dependencies>

3
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java
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@ -87,6 +87,9 @@ public abstract class BaseTest {
/** our log, which we want to capture anything from org.broadinstitute.sting */
public static final Logger logger = CommandLineUtils.getStingLogger();
private static final String CURRENT_DIRECTORY = System.getProperty("user.dir");
public static final String baseDirectory = System.getProperty("basedir", CURRENT_DIRECTORY) + "/";
public static final String hg18Reference = "/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta";
public static final String hg19Reference = "/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta";
public static final String b36KGReference = "/humgen/1kg/reference/human_b36_both.fasta";

4
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java
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@ -49,7 +49,7 @@ public class MD5DB {
*/
private static final int MAX_RECORDS_TO_READ = 1000000;
private static final int MAX_RAW_DIFFS_TO_SUMMARIZE = -1;
public static final String LOCAL_MD5_DB_DIR = "integrationtests";
public static final String LOCAL_MD5_DB_DIR = BaseTest.baseDirectory + "integrationtests";
public static final String GLOBAL_MD5_DB_DIR = "/humgen/gsa-hpprojects/GATK/data/integrationtests";
// tracking and emitting a data file of origina and new md5s
@ -95,7 +95,7 @@ public class MD5DB {
File dir = new File(LOCAL_MD5_DB_DIR);
if ( ! dir.exists() ) {
System.out.printf("##### Creating MD5 db %s%n", LOCAL_MD5_DB_DIR);
if ( ! dir.mkdir() ) {
if ( ! dir.mkdirs() ) {
// Need to check AGAIN whether the dir exists, because we might be doing multi-process parallelism
// within the same working directory, and another GATK instance may have come along and created the
// directory between the calls to exists() and mkdir() above.

1
public/gatk-utils/pom.xml
View File

@ -15,6 +15,7 @@
<properties>
<gatk.basedir>${project.basedir}/../..</gatk.basedir>
<gatk.packagetests.artifactId>gatk-package-distribution</gatk.packagetests.artifactId>
<gsalib.packagedir>org/broadinstitute/gatk/utils/R</gsalib.packagedir>
<gsalib.filename>gsalib.tar.gz</gsalib.filename>
</properties>