From 79f6806bb0634166c93d1eae776fb1391cced24a Mon Sep 17 00:00:00 2001 From: labkey-tchad Date: Tue, 17 Jun 2025 14:41:00 -0700 Subject: [PATCH 1/2] Exclude scijava dependency during server outage --- SequenceAnalysis/build.gradle | 44 +++++++++++++++++------------------ jbrowse/build.gradle | 20 ++++++++-------- 2 files changed, 31 insertions(+), 33 deletions(-) diff --git a/SequenceAnalysis/build.gradle b/SequenceAnalysis/build.gradle index 951b13ae4..51e11cfd8 100644 --- a/SequenceAnalysis/build.gradle +++ b/SequenceAnalysis/build.gradle @@ -1,23 +1,21 @@ -import org.labkey.gradle.plugin.TeamCity import org.labkey.gradle.plugin.extension.ServerDeployExtension import org.labkey.gradle.plugin.extension.TeamCityExtension import org.labkey.gradle.task.DoThenSetup import org.labkey.gradle.util.BuildUtils import org.labkey.gradle.util.GroupNames import org.labkey.gradle.util.PropertiesUtils -import org.labkey.gradle.util.ExternalDependency import java.util.regex.Matcher -repositories { - mavenCentral() - maven { - url "https://maven.scijava.org/content/groups/public/" - content { - includeGroup "cisd" //jhdf5 - } - } -} +//repositories { +// mavenCentral() +// maven { +// url "https://maven.scijava.org/content/groups/public/" +// content { +// includeGroup "cisd" //jhdf5 +// } +// } +//} configurations.all { resolutionStrategy { @@ -91,18 +89,18 @@ dependencies { ) ) - BuildUtils.addExternalDependency( - project, - new ExternalDependency( - 'cisd:jhdf5:19.04.1', - 'JHDF5', - 'JHDF5', - 'https://unlimited.ethz.ch/display/JHDF/', - ExternalDependency.BSD_LICENSE_NAME, - ExternalDependency.BSD_LICENSE_URL, - 'JHDF5 is a Java binding for HDF5. Used by FastQC' - ) - ) +// BuildUtils.addExternalDependency( +// project, +// new ExternalDependency( +// 'cisd:jhdf5:19.04.1', +// 'JHDF5', +// 'JHDF5', +// 'https://unlimited.ethz.ch/display/JHDF/', +// ExternalDependency.BSD_LICENSE_NAME, +// ExternalDependency.BSD_LICENSE_URL, +// 'JHDF5 is a Java binding for HDF5. Used by FastQC' +// ) +// ) BuildUtils.addExternalDependency( project, diff --git a/jbrowse/build.gradle b/jbrowse/build.gradle index a3979a973..4de29862b 100644 --- a/jbrowse/build.gradle +++ b/jbrowse/build.gradle @@ -1,15 +1,15 @@ import org.labkey.gradle.util.BuildUtils; -repositories { - mavenCentral() - maven { - url "https://maven.scijava.org/content/repositories/public/" - content { - // Transitive dependency from SequenceAnalysis - includeGroup "cisd" //jhdf5 - } - } -} +//repositories { +// mavenCentral() +// maven { +// url "https://maven.scijava.org/content/repositories/public/" +// content { +// // Transitive dependency from SequenceAnalysis +// includeGroup "cisd" //jhdf5 +// } +// } +//} dependencies { apiImplementation "com.github.samtools:htsjdk:${htsjdkVersion}" From c161d534b1175c9dca614c9650e1f725af86b2d5 Mon Sep 17 00:00:00 2001 From: labkey-tchad Date: Tue, 17 Jun 2025 14:45:40 -0700 Subject: [PATCH 2/2] Don't optimize dependencies --- SequenceAnalysis/build.gradle | 2 ++ 1 file changed, 2 insertions(+) diff --git a/SequenceAnalysis/build.gradle b/SequenceAnalysis/build.gradle index 51e11cfd8..3b565d682 100644 --- a/SequenceAnalysis/build.gradle +++ b/SequenceAnalysis/build.gradle @@ -1,9 +1,11 @@ +import org.labkey.gradle.plugin.TeamCity import org.labkey.gradle.plugin.extension.ServerDeployExtension import org.labkey.gradle.plugin.extension.TeamCityExtension import org.labkey.gradle.task.DoThenSetup import org.labkey.gradle.util.BuildUtils import org.labkey.gradle.util.GroupNames import org.labkey.gradle.util.PropertiesUtils +import org.labkey.gradle.util.ExternalDependency import java.util.regex.Matcher