From e07befed6df7748539b3edc33041a977374db87b Mon Sep 17 00:00:00 2001 From: Peter van 't Hof Date: Mon, 24 Nov 2014 17:51:33 +0100 Subject: [PATCH] now works with parent poms --- .gitignore | 3 + pom.xml | 102 ++++++++++++++++ protected/basty/pom.xml | 71 ++--------- protected/biopet-gatk-extensions/pom.xml | 71 ++--------- protected/biopet-gatk-pipelines/pom.xml | 71 ++--------- protected/biopet-protected-package/pom.xml | 94 ++------------- .../core/BiopetExecutableProtected.scala | 2 +- protected/pom.xml | 3 - public/bammetrics/pom.xml | 71 ++--------- public/biopet-framework/pom.xml | 113 ++---------------- public/biopet-public-package/pom.xml | 87 ++------------ public/flexiprep/pom.xml | 71 ++--------- public/gentrap/pom.xml | 71 ++--------- public/mapping/pom.xml | 71 ++--------- public/pom.xml | 9 +- public/sage/pom.xml | 71 ++--------- public/yamsvp/pom.xml | 71 ++--------- 17 files changed, 193 insertions(+), 859 deletions(-) diff --git a/.gitignore b/.gitignore index 6fee320e7..8926795a5 100644 --- a/.gitignore +++ b/.gitignore @@ -8,3 +8,6 @@ git.properties *.swp # IntelliJ .idea/workspace.xml +/target/ +/public/target/ +/protected/target/ \ No newline at end of file diff --git a/pom.xml b/pom.xml index fadf3cfb5..70fd9bdde 100644 --- a/pom.xml +++ b/pom.xml @@ -11,4 +11,106 @@ public protected + + + UTF-8 + + + + + + src/main/scripts + + **/* + + + + src/main/resources + + **/* + + + + + + org.scala-tools + maven-scala-plugin + 2.15.2 + + + scala-compile + + compile + testCompile + + + + -dependencyfile + ${project.build.directory}/.scala_dependencies + -deprecation + -feature + + + + + + + org.apache.maven.plugins + maven-jar-plugin + 2.5 + + + + true + true + + + + + + org.apache.maven.plugins + maven-compiler-plugin + 2.3.2 + + true + + + + org.scalariform + scalariform-maven-plugin + 0.1.4 + + + process-sources + + format + + + false + true + 40 + + true + false + false + false + true + false + true + 2 + false + + true + false + false + false + false + false + true + + + + + + diff --git a/protected/basty/pom.xml b/protected/basty/pom.xml index 65d4033c7..c0530b186 100644 --- a/protected/basty/pom.xml +++ b/protected/basty/pom.xml @@ -4,19 +4,17 @@ nl.lumc.sasc Basty - 0.2.0-DEV jar + + nl.lumc.sasc + BiopetGatk + 0.2.0-DEV + ../ + + 2014 Basty - http://maven.apache.org - - - UTF-8 - prepare-package - package - nl.lumc.sasc.biopet.core.BiopetExecutable - @@ -35,59 +33,4 @@ ${project.version} - - - - src/main/resources - - **/* - - - - - - org.scala-tools - maven-scala-plugin - 2.15.2 - - - scala-compile - - compile - testCompile - - - - -dependencyfile - ${project.build.directory}/.scala_dependencies - -deprecation - -feature - - - - - - - org.apache.maven.plugins - maven-jar-plugin - 2.5 - - - - true - true - - - - - - org.apache.maven.plugins - maven-compiler-plugin - 2.3.2 - - true - - - - diff --git a/protected/biopet-gatk-extensions/pom.xml b/protected/biopet-gatk-extensions/pom.xml index ca7e60e3b..0f990f581 100644 --- a/protected/biopet-gatk-extensions/pom.xml +++ b/protected/biopet-gatk-extensions/pom.xml @@ -4,19 +4,17 @@ nl.lumc.sasc BiopetGatkExtensions - 0.2.0-DEV jar + + nl.lumc.sasc + BiopetGatk + 0.2.0-DEV + ../ + + 2014 BiopetGatkExtensions - http://maven.apache.org - - - UTF-8 - prepare-package - package - nl.lumc.sasc.biopet.core.BiopetExecutable - @@ -30,59 +28,4 @@ 3.3 - - - - src/main/resources - - **/* - - - - - - org.scala-tools - maven-scala-plugin - 2.15.2 - - - scala-compile - - compile - testCompile - - - - -dependencyfile - ${project.build.directory}/.scala_dependencies - -deprecation - -feature - - - - - - - org.apache.maven.plugins - maven-jar-plugin - 2.5 - - - - true - true - - - - - - org.apache.maven.plugins - maven-compiler-plugin - 2.3.2 - - true - - - - diff --git a/protected/biopet-gatk-pipelines/pom.xml b/protected/biopet-gatk-pipelines/pom.xml index 946d56a47..3db46628e 100644 --- a/protected/biopet-gatk-pipelines/pom.xml +++ b/protected/biopet-gatk-pipelines/pom.xml @@ -4,19 +4,17 @@ nl.lumc.sasc BiopetGatkPipelines - 0.2.0-DEV jar + + nl.lumc.sasc + BiopetGatk + 0.2.0-DEV + ../ + + 2014 BiopetGatkPipelines - http://maven.apache.org - - - UTF-8 - prepare-package - package - nl.lumc.sasc.biopet.core.BiopetExecutable - @@ -35,59 +33,4 @@ ${project.version} - - - - src/main/resources - - **/* - - - - - - org.scala-tools - maven-scala-plugin - 2.15.2 - - - scala-compile - - compile - testCompile - - - - -dependencyfile - ${project.build.directory}/.scala_dependencies - -deprecation - -feature - - - - - - - org.apache.maven.plugins - maven-jar-plugin - 2.5 - - - - true - true - - - - - - org.apache.maven.plugins - maven-compiler-plugin - 2.3.2 - - true - - - - diff --git a/protected/biopet-protected-package/pom.xml b/protected/biopet-protected-package/pom.xml index 883c98b3e..6c3c5a8df 100644 --- a/protected/biopet-protected-package/pom.xml +++ b/protected/biopet-protected-package/pom.xml @@ -4,20 +4,17 @@ nl.lumc.sasc BiopetProtectedPackage - 0.2.0-DEV jar + + nl.lumc.sasc + BiopetGatk + 0.2.0-DEV + ../ + + 2014 BiopetProtectedPackage - http://maven.apache.org - - - UTF-8 - prepare-package - package - nl.lumc.sasc.biopet.core.BiopetExecutableProtected - - @@ -42,84 +39,7 @@ - - - src/main/resources - - **/* - - - - - org.scala-tools - maven-scala-plugin - 2.15.2 - - - scala-compile - - compile - testCompile - - - - -dependencyfile - ${project.build.directory}/.scala_dependencies - -deprecation - -feature - - - - - - - pl.project13.maven - git-commit-id-plugin - 2.1.10 - - - - revision - - - - - - git - dd.MM.yyyy '@' HH:mm:ss z - false - true - ${project.basedir}/../../.git - false - true - src/main/resources/git.properties - false - 7 - false - - - false - false - 7 - -dirty - false - - - - - org.apache.maven.plugins - maven-jar-plugin - 2.5 - - - - true - true - - - - org.apache.maven.plugins maven-shade-plugin diff --git a/protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutableProtected.scala b/protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutableProtected.scala index 377533dc9..e09dd7f2b 100644 --- a/protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutableProtected.scala +++ b/protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutableProtected.scala @@ -9,6 +9,6 @@ object BiopetExecutableProtected extends BiopetExecutable { nl.lumc.sasc.biopet.pipelines.gatk.GatkVariantRecalibration, nl.lumc.sasc.biopet.pipelines.gatk.GatkVcfSampleCompare, nl.lumc.sasc.biopet.pipelines.basty.Basty) - + def tools = BiopetExecutablePublic.tools } \ No newline at end of file diff --git a/protected/pom.xml b/protected/pom.xml index 2a4c245d2..ffb482a5c 100644 --- a/protected/pom.xml +++ b/protected/pom.xml @@ -16,7 +16,4 @@ basty biopet-protected-package - - UTF-8 - \ No newline at end of file diff --git a/public/bammetrics/pom.xml b/public/bammetrics/pom.xml index 715aaf48f..66f101948 100644 --- a/public/bammetrics/pom.xml +++ b/public/bammetrics/pom.xml @@ -4,19 +4,17 @@ nl.lumc.sasc BamMetrics - 0.2.0-DEV jar + + nl.lumc.sasc + Biopet + 0.2.0-DEV + ../ + + 2014 BamMetrics - http://maven.apache.org - - - UTF-8 - prepare-package - package - nl.lumc.sasc.biopet.core.BiopetExecutable - @@ -25,59 +23,4 @@ ${project.version} - - - - src/main/resources - - **/* - - - - - - org.scala-tools - maven-scala-plugin - 2.15.2 - - - scala-compile - - compile - testCompile - - - - -dependencyfile - ${project.build.directory}/.scala_dependencies - -deprecation - -feature - - - - - - - org.apache.maven.plugins - maven-jar-plugin - 2.5 - - - - true - true - - - - - - org.apache.maven.plugins - maven-compiler-plugin - 2.3.2 - - true - - - - diff --git a/public/biopet-framework/pom.xml b/public/biopet-framework/pom.xml index 5cdd6c5cf..9616ae319 100644 --- a/public/biopet-framework/pom.xml +++ b/public/biopet-framework/pom.xml @@ -4,19 +4,17 @@ nl.lumc.sasc BiopetFramework - 0.2.0-DEV jar + + nl.lumc.sasc + Biopet + 0.2.0-DEV + ../ + + 2014 BiopetFramework - http://maven.apache.org - - - UTF-8 - prepare-package - package - nl.lumc.sasc.biopet.core.BiopetExecutable - @@ -96,101 +94,4 @@ 3.2.0 - - - - src/main/scripts - - **/* - - - - src/main/resources - - **/* - - - - - - org.scala-tools - maven-scala-plugin - 2.15.2 - - - scala-compile - - compile - testCompile - - - - -dependencyfile - ${project.build.directory}/.scala_dependencies - -deprecation - -feature - - - - - - - org.apache.maven.plugins - maven-jar-plugin - 2.5 - - - - true - true - - - - - - org.apache.maven.plugins - maven-compiler-plugin - 2.3.2 - - true - - - - org.scalariform - scalariform-maven-plugin - 0.1.4 - - - process-sources - - format - - - false - true - 40 - - true - false - false - false - true - false - true - 2 - false - - true - false - false - false - false - false - true - - - - - - diff --git a/public/biopet-public-package/pom.xml b/public/biopet-public-package/pom.xml index 650f61a86..f2a906590 100644 --- a/public/biopet-public-package/pom.xml +++ b/public/biopet-public-package/pom.xml @@ -4,16 +4,20 @@ nl.lumc.sasc BiopetPublicPackage - 0.2.0-DEV jar + + nl.lumc.sasc + Biopet + 0.2.0-DEV + ../ + + 2014 BiopetPublicPackage http://maven.apache.org - UTF-8 - prepare-package package nl.lumc.sasc.biopet.core.BiopetExecutablePublic @@ -57,84 +61,7 @@ - - - src/main/resources - - **/* - - - - - org.scala-tools - maven-scala-plugin - 2.15.2 - - - scala-compile - - compile - testCompile - - - - -dependencyfile - ${project.build.directory}/.scala_dependencies - -deprecation - -feature - - - - - - - pl.project13.maven - git-commit-id-plugin - 2.1.10 - - - - revision - - - - - - git - dd.MM.yyyy '@' HH:mm:ss z - false - true - ${project.basedir}/../../.git - false - true - src/main/resources/git.properties - false - 7 - false - - - false - false - 7 - -dirty - false - - - - - org.apache.maven.plugins - maven-jar-plugin - 2.5 - - - - true - true - - - - org.apache.maven.plugins maven-shade-plugin diff --git a/public/flexiprep/pom.xml b/public/flexiprep/pom.xml index e87252044..32bdae80c 100644 --- a/public/flexiprep/pom.xml +++ b/public/flexiprep/pom.xml @@ -4,19 +4,17 @@ nl.lumc.sasc Flexiprep - 0.2.0-DEV jar + + nl.lumc.sasc + Biopet + 0.2.0-DEV + ../ + + 2014 Flexiprep - http://maven.apache.org - - - UTF-8 - prepare-package - package - nl.lumc.sasc.biopet.core.BiopetExecutable - @@ -25,59 +23,4 @@ ${project.version} - - - - src/main/resources - - **/* - - - - - - org.scala-tools - maven-scala-plugin - 2.15.2 - - - scala-compile - - compile - testCompile - - - - -dependencyfile - ${project.build.directory}/.scala_dependencies - -deprecation - -feature - - - - - - - org.apache.maven.plugins - maven-jar-plugin - 2.5 - - - - true - true - - - - - - org.apache.maven.plugins - maven-compiler-plugin - 2.3.2 - - true - - - - diff --git a/public/gentrap/pom.xml b/public/gentrap/pom.xml index e205a7d60..2ce5f8b8c 100644 --- a/public/gentrap/pom.xml +++ b/public/gentrap/pom.xml @@ -4,19 +4,17 @@ nl.lumc.sasc Gentrap - 0.2.0-DEV jar + + nl.lumc.sasc + Biopet + 0.2.0-DEV + ../ + + 2014 Gentrap - http://maven.apache.org - - - UTF-8 - prepare-package - package - nl.lumc.sasc.biopet.core.BiopetExecutable - @@ -30,59 +28,4 @@ ${project.version} - - - - src/main/resources - - **/* - - - - - - org.scala-tools - maven-scala-plugin - 2.15.2 - - - scala-compile - - compile - testCompile - - - - -dependencyfile - ${project.build.directory}/.scala_dependencies - -deprecation - -feature - - - - - - - org.apache.maven.plugins - maven-jar-plugin - 2.5 - - - - true - true - - - - - - org.apache.maven.plugins - maven-compiler-plugin - 2.3.2 - - true - - - - diff --git a/public/mapping/pom.xml b/public/mapping/pom.xml index c774123be..75d669a75 100644 --- a/public/mapping/pom.xml +++ b/public/mapping/pom.xml @@ -4,19 +4,17 @@ nl.lumc.sasc Mapping - 0.2.0-DEV jar + + nl.lumc.sasc + Biopet + 0.2.0-DEV + ../ + + 2014 Mapping - http://maven.apache.org - - - UTF-8 - prepare-package - package - nl.lumc.sasc.biopet.core.BiopetExecutable - @@ -35,59 +33,4 @@ ${project.version} - - - - src/main/resources - - **/* - - - - - - org.scala-tools - maven-scala-plugin - 2.15.2 - - - scala-compile - - compile - testCompile - - - - -dependencyfile - ${project.build.directory}/.scala_dependencies - -deprecation - -feature - - - - - - - org.apache.maven.plugins - maven-jar-plugin - 2.5 - - - - true - true - - - - - - org.apache.maven.plugins - maven-compiler-plugin - 2.3.2 - - true - - - - diff --git a/public/pom.xml b/public/pom.xml index 79ff4c515..2dd56dbcb 100644 --- a/public/pom.xml +++ b/public/pom.xml @@ -1,18 +1,15 @@ 4.0.0 + Biopet + Biopet + pom nl.lumc.sasc BiopetRoot 0.2.0-DEV ../ - Biopet - Biopet - pom - - UTF-8 - biopet-framework biopet-public-package diff --git a/public/sage/pom.xml b/public/sage/pom.xml index 89247d5e5..0b91859d6 100644 --- a/public/sage/pom.xml +++ b/public/sage/pom.xml @@ -4,19 +4,17 @@ nl.lumc.sasc Sage - 0.2.0-DEV jar + + nl.lumc.sasc + Biopet + 0.2.0-DEV + ../ + + 2014 Sage - http://maven.apache.org - - - UTF-8 - prepare-package - package - nl.lumc.sasc.biopet.core.BiopetExecutable - @@ -30,59 +28,4 @@ ${project.version} - - - - src/main/resources - - **/* - - - - - - org.scala-tools - maven-scala-plugin - 2.15.2 - - - scala-compile - - compile - testCompile - - - - -dependencyfile - ${project.build.directory}/.scala_dependencies - -deprecation - -feature - - - - - - - org.apache.maven.plugins - maven-jar-plugin - 2.5 - - - - true - true - - - - - - org.apache.maven.plugins - maven-compiler-plugin - 2.3.2 - - true - - - - diff --git a/public/yamsvp/pom.xml b/public/yamsvp/pom.xml index 355fa554e..a590cd3df 100644 --- a/public/yamsvp/pom.xml +++ b/public/yamsvp/pom.xml @@ -4,19 +4,17 @@ nl.lumc.sasc Yamsvp - 0.2.0-DEV jar + + nl.lumc.sasc + Biopet + 0.2.0-DEV + ../ + + 2014 Yamsvp - http://maven.apache.org - - - UTF-8 - prepare-package - package - nl.lumc.sasc.biopet.core.BiopetExecutable - @@ -30,59 +28,4 @@ ${project.version} - - - - src/main/resources - - **/* - - - - - - org.scala-tools - maven-scala-plugin - 2.15.2 - - - scala-compile - - compile - testCompile - - - - -dependencyfile - ${project.build.directory}/.scala_dependencies - -deprecation - -feature - - - - - - - org.apache.maven.plugins - maven-jar-plugin - 2.5 - - - - true - true - - - - - - org.apache.maven.plugins - maven-compiler-plugin - 2.3.2 - - true - - - - -- GitLab