From f7ce0d7abdb653fc82148f89290a73f6eb79b9f5 Mon Sep 17 00:00:00 2001 From: Louis Bergelson Date: Fri, 14 Jul 2023 16:23:08 -0400 Subject: [PATCH 1/3] Update dependencies to latest versions --- build.gradle | 22 ++++++++++++---------- 1 file changed, 12 insertions(+), 10 deletions(-) diff --git a/build.gradle b/build.gradle index b06a233bf5..e33c390a2b 100644 --- a/build.gradle +++ b/build.gradle @@ -57,23 +57,25 @@ def ensureBuildPrerequisites(buildPrerequisitesMessage) { ensureBuildPrerequisites(buildPrerequisitesMessage) -final htsjdkVersion = System.getProperty('htsjdk.version', '3.0.1') +final htsjdkVersion = System.getProperty('htsjdk.version', '3.0.5') dependencies { - implementation('com.intel.gkl:gkl:0.8.8') { + implementation('com.intel.gkl:gkl:0.8.11') { exclude module: 'htsjdk' } - implementation 'com.google.guava:guava:15.0' - implementation 'org.apache.commons:commons-math3:3.5' - implementation 'org.apache.commons:commons-collections4:4.3' + implementation 'com.google.guava:guava:31.1-jre' + implementation 'org.apache.commons:commons-math3:3.6.1' + implementation 'org.apache.commons:commons-collections4:4.4' implementation 'com.github.samtools:htsjdk:' + htsjdkVersion implementation 'org.broadinstitute:barclay:5.0.0' - implementation 'org.apache.logging.log4j:log4j-api:2.17.1' - implementation 'org.apache.logging.log4j:log4j-core:2.17.1' + implementation 'org.apache.logging.log4j:log4j-api:2.20.0' + implementation 'org.apache.logging.log4j:log4j-core:2.20.0' implementation 'org.openjdk.nashorn:nashorn-core:15.4' - implementation 'org.apache.commons:commons-lang3:3.6' - implementation 'com.google.cloud:google-cloud-nio:0.123.25' + implementation 'org.apache.commons:commons-lang3:3.12.0' + implementation 'com.google.cloud:google-cloud-nio:0.126.9' + implementation 'commons-io:commons-io:2.11.0' + implementation 'org.broadinstitute:gatk-native-bindings:1.0.0' - testImplementation 'org.testng:testng:6.14.3' + testImplementation 'org.testng:testng:7.7.0' } configurations.all { From 893d671a712a2003f389407d21508a037178548c Mon Sep 17 00:00:00 2001 From: Louis Bergelson Date: Thu, 27 Jul 2023 13:26:40 -0400 Subject: [PATCH 2/3] Update build.gradle --- build.gradle | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle b/build.gradle index 7d62b6a946..9791832a8c 100644 --- a/build.gradle +++ b/build.gradle @@ -65,7 +65,7 @@ dependencies { exclude module: 'htsjdk' } - implementation 'com.google.guava:guava:32.1-jre' + implementation 'com.google.guava:guava:32.1.1-jre' implementation 'org.apache.commons:commons-math3:3.6.1' implementation 'org.apache.commons:commons-collections4:4.4' implementation 'com.github.samtools:htsjdk:' + htsjdkVersion From 5b5f7acbb4f3fc1b616f206981661a3fc7987dd3 Mon Sep 17 00:00:00 2001 From: Louis Bergelson Date: Thu, 27 Jul 2023 13:28:23 -0400 Subject: [PATCH 3/3] Update build.gradle --- build.gradle | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle b/build.gradle index 9791832a8c..bf4f557b3f 100644 --- a/build.gradle +++ b/build.gradle @@ -64,6 +64,7 @@ dependencies { implementation('com.intel.gkl:gkl:0.8.11') { exclude module: 'htsjdk' } + implementation 'org.broadinstitute:gatk-native-bindings:1.0.0' //this should be redundant when GKL is updated past 0.8.11 implementation 'com.google.guava:guava:32.1.1-jre' implementation 'org.apache.commons:commons-math3:3.6.1' @@ -76,7 +77,6 @@ dependencies { implementation 'org.apache.commons:commons-lang3:3.12.0' implementation 'com.google.cloud:google-cloud-nio:0.127.0' implementation 'commons-io:commons-io:2.11.0' - implementation 'org.broadinstitute:gatk-native-bindings:1.0.0' testImplementation 'org.testng:testng:7.7.0' }