From 5e7ffea7eba4e18515c281c0b71ff774ba375769 Mon Sep 17 00:00:00 2001 From: labkey-susanh Date: Mon, 18 Apr 2022 08:58:00 -0700 Subject: [PATCH 1/4] Add external maven repositories --- primeseq/build.gradle | 15 +++++++++++++++ tcrdb/build.gradle | 15 +++++++++++++++ variantdb/build.gradle | 12 ++++++++++++ 3 files changed, 42 insertions(+) diff --git a/primeseq/build.gradle b/primeseq/build.gradle index 0d7767f20..96a114419 100644 --- a/primeseq/build.gradle +++ b/primeseq/build.gradle @@ -1,5 +1,20 @@ import org.labkey.gradle.util.BuildUtils; +repositories { + mavenCentral() + maven { + url "https://clojars.org/repo" + } + // Added for org.clojars.chapmanb:sam dependency required by com.github.samtools:htsjdk + maven { + url "https://maven.scijava.org/content/groups/public" + } + // Added for opencharts dependency (required by biojava) + maven { + url "https://repository.jboss.org/nexus/content/repositories/thirdparty-releases/" + } +} + dependencies { implementation "com.github.samtools:htsjdk:${htsjdkVersion}" implementation "net.sf.opencsv:opencsv:${opencsvVersion}" diff --git a/tcrdb/build.gradle b/tcrdb/build.gradle index de1b8d419..e111c096c 100644 --- a/tcrdb/build.gradle +++ b/tcrdb/build.gradle @@ -1,5 +1,20 @@ import org.labkey.gradle.util.BuildUtils; +repositories { + mavenCentral() + maven { + url "https://clojars.org/repo" + } + // Added for org.clojars.chapmanb:sam dependency required by com.github.samtools:htsjdk + maven { + url "https://maven.scijava.org/content/groups/public" + } + // Added for opencharts dependency (required by biojava) + maven { + url "https://repository.jboss.org/nexus/content/repositories/thirdparty-releases/" + } +} + dependencies { BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:singlecell", depProjectConfig: "apiJarFile") BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:SequenceAnalysis", depProjectConfig: "apiJarFile") diff --git a/variantdb/build.gradle b/variantdb/build.gradle index 3752d3158..cb6426250 100644 --- a/variantdb/build.gradle +++ b/variantdb/build.gradle @@ -1,5 +1,17 @@ import org.labkey.gradle.util.BuildUtils; +repositories { + mavenCentral() + // Added for org.clojars.chapmanb:sam dependency required by com.github.samtools:htsjdk + maven { + url "https://clojars.org/repo" + } + // Added for opencharts dependency (required by biojava) + maven { + url "https://repository.jboss.org/nexus/content/repositories/thirdparty-releases/" + } +} + dependencies { implementation "com.github.samtools:htsjdk:${htsjdkVersion}" external "commons-net:commons-net:${commonsNetVersion}" From 14b1fb4de0291ec9ec74d95386ea1dbd5e990fdc Mon Sep 17 00:00:00 2001 From: labkey-susanh Date: Mon, 18 Apr 2022 13:15:25 -0700 Subject: [PATCH 2/4] remove jboss repository (not needed for this version) --- primeseq/build.gradle | 4 ---- tcrdb/build.gradle | 4 ---- variantdb/build.gradle | 4 ---- 3 files changed, 12 deletions(-) diff --git a/primeseq/build.gradle b/primeseq/build.gradle index 96a114419..331b27176 100644 --- a/primeseq/build.gradle +++ b/primeseq/build.gradle @@ -9,10 +9,6 @@ repositories { maven { url "https://maven.scijava.org/content/groups/public" } - // Added for opencharts dependency (required by biojava) - maven { - url "https://repository.jboss.org/nexus/content/repositories/thirdparty-releases/" - } } dependencies { diff --git a/tcrdb/build.gradle b/tcrdb/build.gradle index e111c096c..dd30ea440 100644 --- a/tcrdb/build.gradle +++ b/tcrdb/build.gradle @@ -9,10 +9,6 @@ repositories { maven { url "https://maven.scijava.org/content/groups/public" } - // Added for opencharts dependency (required by biojava) - maven { - url "https://repository.jboss.org/nexus/content/repositories/thirdparty-releases/" - } } dependencies { diff --git a/variantdb/build.gradle b/variantdb/build.gradle index cb6426250..d260381fe 100644 --- a/variantdb/build.gradle +++ b/variantdb/build.gradle @@ -6,10 +6,6 @@ repositories { maven { url "https://clojars.org/repo" } - // Added for opencharts dependency (required by biojava) - maven { - url "https://repository.jboss.org/nexus/content/repositories/thirdparty-releases/" - } } dependencies { From 8e4dd1b7104e6d11d2b6cf0ab63ec6c667be2673 Mon Sep 17 00:00:00 2001 From: labkey-susanh Date: Mon, 18 Apr 2022 14:45:40 -0700 Subject: [PATCH 3/4] remove scijava repo --- primeseq/build.gradle | 7 ++++--- tcrdb/build.gradle | 8 ++++---- 2 files changed, 8 insertions(+), 7 deletions(-) diff --git a/primeseq/build.gradle b/primeseq/build.gradle index 331b27176..d27d907f2 100644 --- a/primeseq/build.gradle +++ b/primeseq/build.gradle @@ -2,13 +2,14 @@ import org.labkey.gradle.util.BuildUtils; repositories { mavenCentral() + // Added for org.clojars.chapmanb:sam dependency required by com.github.samtools:htsjdk maven { url "https://clojars.org/repo" } // Added for org.clojars.chapmanb:sam dependency required by com.github.samtools:htsjdk - maven { - url "https://maven.scijava.org/content/groups/public" - } + //maven { + // url "https://maven.scijava.org/content/groups/public" + //} } dependencies { diff --git a/tcrdb/build.gradle b/tcrdb/build.gradle index dd30ea440..f4bcb07eb 100644 --- a/tcrdb/build.gradle +++ b/tcrdb/build.gradle @@ -2,13 +2,13 @@ import org.labkey.gradle.util.BuildUtils; repositories { mavenCentral() - maven { - url "https://clojars.org/repo" - } // Added for org.clojars.chapmanb:sam dependency required by com.github.samtools:htsjdk maven { - url "https://maven.scijava.org/content/groups/public" + url "https://clojars.org/repo" } + //maven { + // url "https://maven.scijava.org/content/groups/public" + //} } dependencies { From 5c3ba5f15d764c19fff58dd74cc79053d051eee7 Mon Sep 17 00:00:00 2001 From: labkey-susanh Date: Mon, 18 Apr 2022 15:59:46 -0700 Subject: [PATCH 4/4] remove commented out repo --- primeseq/build.gradle | 4 ---- tcrdb/build.gradle | 3 --- 2 files changed, 7 deletions(-) diff --git a/primeseq/build.gradle b/primeseq/build.gradle index d27d907f2..1a8b44122 100644 --- a/primeseq/build.gradle +++ b/primeseq/build.gradle @@ -6,10 +6,6 @@ repositories { maven { url "https://clojars.org/repo" } - // Added for org.clojars.chapmanb:sam dependency required by com.github.samtools:htsjdk - //maven { - // url "https://maven.scijava.org/content/groups/public" - //} } dependencies { diff --git a/tcrdb/build.gradle b/tcrdb/build.gradle index f4bcb07eb..44b61bd11 100644 --- a/tcrdb/build.gradle +++ b/tcrdb/build.gradle @@ -6,9 +6,6 @@ repositories { maven { url "https://clojars.org/repo" } - //maven { - // url "https://maven.scijava.org/content/groups/public" - //} } dependencies {