From 8abcb0b037333f5924940393e186737b82a77f18 Mon Sep 17 00:00:00 2001 From: labkey-tchad Date: Tue, 17 Jun 2025 14:51:59 -0700 Subject: [PATCH 1/2] Disable scijava dependency during server outage --- SequenceAnalysis/build.gradle | 42 +++++++++++++++++------------------ jbrowse/build.gradle | 20 ++++++++--------- 2 files changed, 31 insertions(+), 31 deletions(-) diff --git a/SequenceAnalysis/build.gradle b/SequenceAnalysis/build.gradle index 951b13ae4..3b565d682 100644 --- a/SequenceAnalysis/build.gradle +++ b/SequenceAnalysis/build.gradle @@ -9,15 +9,15 @@ 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 +91,18 @@ 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 3a5f1b6a34d1199b41988403a02a3b63755d9020 Mon Sep 17 00:00:00 2001 From: labkey-tchad Date: Tue, 17 Jun 2025 16:38:26 -0700 Subject: [PATCH 2/2] Try to pull jhdf from Artifactory --- SequenceAnalysis/build.gradle | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/SequenceAnalysis/build.gradle b/SequenceAnalysis/build.gradle index 3b565d682..b3b486d2a 100644 --- a/SequenceAnalysis/build.gradle +++ b/SequenceAnalysis/build.gradle @@ -91,18 +91,18 @@ 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,