Steffen Möller pushed to branch master at Debian Med / picard-tools
Commits: 5e179c29 by Steffen Moeller at 2020-09-12T01:12:01+02:00 Fix Manifest - - - - - 4 changed files: - debian/changelog - debian/libpicard-java.manifest - debian/patches/30-tests-fix-dataprovider.patch - debian/rules Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,9 @@ +picard-tools (2.23.4+dfsg-2) unstable; urgency=medium + + * Fixed classpath in picard.jar Manifest (s/:/ /g) + + -- Steffen Moeller <[email protected]> Fri, 11 Sep 2020 23:40:02 +0200 + picard-tools (2.23.4+dfsg-1) unstable; urgency=medium [ Michael R. Crusoe ] ===================================== debian/libpicard-java.manifest ===================================== @@ -1,3 +1,3 @@ usr/share/java/picard.jar: Main-Class: picard.cmdline.PicardCommandLine - Class-Path: /usr/share/java/htsjdk.jar:/usr/share/java/guava.jar:/usr/lib/jvm/default-java/lib/tools.jar:/usr/share/java/commons-lang3.jar:/usr/share/java/gkl.jar:/usr/share/java/gatk-native-bindings.jar:/usr/share/java/barclay.jar + Class-Path: /usr/share/java/htsjdk.jar /usr/share/java/guava.jar /usr/lib/jvm/default-java/lib/tools.jar /usr/share/java/commons-lang3.jar /usr/share/java/gkl.jar /usr/share/java/gatk-native-bindings.jar /usr/share/java/barclay.jar ===================================== debian/patches/30-tests-fix-dataprovider.patch ===================================== @@ -1,8 +1,10 @@ Description: fix data provider requirements Author: Sascha Steinbiss <[email protected]> +Index: picard-tools/src/test/java/picard/analysis/directed/CollectHsMetricsTest.java +=================================================================== --- picard-tools.orig/src/test/java/picard/analysis/directed/CollectHsMetricsTest.java +++ picard-tools/src/test/java/picard/analysis/directed/CollectHsMetricsTest.java -@@ -31,33 +31,33 @@ +@@ -31,33 +31,33 @@ public class CollectHsMetricsTest extend @DataProvider(name = "collectHsMetricsDataProvider") public Object[][] targetedIntervalDataProvider() { @@ -50,7 +52,7 @@ Author: Sascha Steinbiss <[email protected]> }; } -@@ -99,7 +99,7 @@ +@@ -99,7 +99,7 @@ public class CollectHsMetricsTest extend final long pfBases, final int sampleSize) throws IOException { @@ -59,7 +61,7 @@ Author: Sascha Steinbiss <[email protected]> outfile.deleteOnExit(); final String[] args = new String[] { -@@ -141,14 +141,14 @@ +@@ -141,14 +141,14 @@ public class CollectHsMetricsTest extend * Test that the depth histogram is [10,10,0,...,0] */ @@ -77,9 +79,11 @@ Author: Sascha Steinbiss <[email protected]> outfile.deleteOnExit(); final String[] args = new String[] { +Index: picard-tools/src/test/java/picard/util/IntervalListToolsTest.java +=================================================================== --- picard-tools.orig/src/test/java/picard/util/IntervalListToolsTest.java +++ picard-tools/src/test/java/picard/util/IntervalListToolsTest.java -@@ -173,7 +173,6 @@ +@@ -173,7 +173,6 @@ public class IntervalListToolsTest exten }; } @@ -87,9 +91,11 @@ Author: Sascha Steinbiss <[email protected]> public void testActionsWithUnique(final IntervalListTools.Action action, final long bases, final int intervals) throws IOException { final IntervalList il = tester(action, false, true); Assert.assertEquals(il.getBaseCount(), bases, "unexpected number of bases found."); +Index: picard-tools/src/test/java/picard/fingerprint/FingerprintCheckerTest.java +=================================================================== --- picard-tools.orig/src/test/java/picard/fingerprint/FingerprintCheckerTest.java +++ picard-tools/src/test/java/picard/fingerprint/FingerprintCheckerTest.java -@@ -102,7 +102,6 @@ +@@ -102,7 +102,6 @@ public class FingerprintCheckerTest { }; } @@ -97,7 +103,7 @@ Author: Sascha Steinbiss <[email protected]> public void testCheckFingerprintsVcf(final File vcfFile, final File genotypesFile, final String observedSampleAlias, final String expectedSampleAlias, final double llExpectedSample, final double llRandomSample, final double lodExpectedSample) throws IOException { final Path indexedInputVcf = VcfTestUtils.createTemporaryIndexedVcfFromInput(vcfFile, "fingerprintcheckertest.tmp.").toPath(); -@@ -124,7 +123,6 @@ +@@ -124,7 +123,6 @@ public class FingerprintCheckerTest { Assert.assertEquals(mr.getLOD(), lodExpectedSample, DELTA); } @@ -105,7 +111,7 @@ Author: Sascha Steinbiss <[email protected]> public void testFingerprintVcf(final File vcfFile, final File genotypesFile, final String observedSampleAlias, final String expectedSampleAlias, final double llExpectedSample, final double llRandomSample, final double lodExpectedSample) { final FingerprintChecker fpChecker = new FingerprintChecker(SUBSETTED_HAPLOTYPE_DATABASE_FOR_TESTING); -@@ -133,7 +131,6 @@ +@@ -133,7 +131,6 @@ public class FingerprintCheckerTest { Assert.assertFalse(fp1.isEmpty()); } @@ -113,16 +119,18 @@ Author: Sascha Steinbiss <[email protected]> public void testFingerprintSwapEqual(final File vcfFile, final File genotypesFile, final String observedSampleAlias, final String expectedSampleAlias, final double llExpectedSample, final double llRandomSample, final double lodExpectedSample) { final FingerprintChecker fpChecker = new FingerprintChecker(SUBSETTED_HAPLOTYPE_DATABASE_FOR_TESTING); -@@ -476,4 +473,4 @@ +@@ -491,4 +488,4 @@ public class FingerprintCheckerTest { VcfTestUtils.assertVcfFilesAreEqual(vcfOutput, vcfExpected); } -} \ No newline at end of file +} +Index: picard-tools/src/test/java/picard/arrays/illumina/InfiniumDataFileTest.java +=================================================================== --- picard-tools.orig/src/test/java/picard/arrays/illumina/InfiniumDataFileTest.java +++ picard-tools/src/test/java/picard/arrays/illumina/InfiniumDataFileTest.java -@@ -21,13 +21,11 @@ +@@ -21,13 +21,11 @@ public class InfiniumDataFileTest { }; } ===================================== debian/rules ===================================== @@ -18,6 +18,8 @@ override_dh_auto_build: override_dh_auto_test: ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) + # ensure the .jar can be executed + /usr/bin/java -XX:ParallelGCThreads=1 -Xmx4G -Xss16M -Djava.io.tmpdir=/tmp -jar `find . -name "picard*.jar" BamIndexStats|head -n 1` -h > /dev/null # Tests do not work with locales with a different decimal separator # (for example ',') env LC_ALL=C \ View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/commit/5e179c294f3840f5f9c2edc282332af3f4aecfbe -- View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/commit/5e179c294f3840f5f9c2edc282332af3f4aecfbe You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
