GELOG / variantminer

A web UI over genomic data
Apache License 2.0
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Package adam-ids in executable jar #20

Open iki-v opened 9 years ago

iki-v commented 9 years ago

Comme discuté, j'ai fait le necessaire pour packager le projet dans un jar executable. La wiki du projet detail la demarche à suivre pour l'utiliser : https://github.com/GELOG/adam-ibs.

davidonlaptop commented 9 years ago

See also:

https://github.com/GELOG/adam-ibs/issues/50 https://github.com/GELOG/adam-ibs/issues/51

iki-v commented 9 years ago

La première option décrite dans wiki build n'est pas suffisamment "single" ?

davidonlaptop commented 9 years ago

Pour l'instant, ca ne fonctionne pas.

iki-v commented 9 years ago

Et chez moi ça fonctionne :

[INFO] Scanning for projects... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] Adam IBS [INFO] Adam IBS Data [INFO] Adam IBS Core [INFO]
[INFO] ------------------------------------------------------------------------ [INFO] Building Adam IBS 0.1.0 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ adam-ibs --- [INFO] [INFO] --- maven-install-plugin:2.3.1:install (default-install) @ adam-ibs --- [INFO] Installing /home/ikizema/DEV/PROJECTS/personal/adam-ibs-last/pom.xml to /home/ikizema/.m2/repository/com/ets/mgl804/adam-ibs/0.1.0/adam-ibs-0.1.0.pom [INFO]
[INFO] ------------------------------------------------------------------------ [INFO] Building Adam IBS Data 0.1.0 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ adam-ibs-data --- [INFO] [INFO] --- avro-maven-plugin:1.7.7:schema (schemas) @ adam-ibs-data --- [INFO] [INFO] --- avro-maven-plugin:1.7.7:protocol (schemas) @ adam-ibs-data --- [INFO] [INFO] --- avro-maven-plugin:1.7.7:idl-protocol (schemas) @ adam-ibs-data --- [WARNING] Avro: Invalid default for field id: "unknown" not a "int" [WARNING] Avro: Invalid default for field sender: "unknown" not a "int" [WARNING] Avro: Invalid default for field recipient: "unknown" not a "int" [WARNING] Avro: Invalid default for field id: "unknown" not a "int" [WARNING] Avro: Invalid default for field sender: "unknown" not a "int" [WARNING] Avro: Invalid default for field recipient: "unknown" not a "int" [INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ adam-ibs-data --- [debug] execute contextualize [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:2.3.2:compile (default-compile) @ adam-ibs-data --- [INFO] Compiling 29 source files to /home/ikizema/DEV/PROJECTS/personal/adam-ibs-last/adam-ibs-data/target/classes [INFO] [INFO] --- avro-maven-plugin:1.7.7:schema (schemas) @ adam-ibs-data --- [INFO] [INFO] --- avro-maven-plugin:1.7.7:protocol (schemas) @ adam-ibs-data --- [INFO] [INFO] --- avro-maven-plugin:1.7.7:idl-protocol (schemas) @ adam-ibs-data --- [WARNING] Avro: Invalid default for field id: "unknown" not a "int" [WARNING] Avro: Invalid default for field sender: "unknown" not a "int" [WARNING] Avro: Invalid default for field recipient: "unknown" not a "int" [WARNING] Avro: Invalid default for field id: "unknown" not a "int" [WARNING] Avro: Invalid default for field sender: "unknown" not a "int" [WARNING] Avro: Invalid default for field recipient: "unknown" not a "int" [INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ adam-ibs-data --- [debug] execute contextualize [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:2.3.2:compile (default-compile) @ adam-ibs-data --- [INFO] Compiling 12 source files to /home/ikizema/DEV/PROJECTS/personal/adam-ibs-last/adam-ibs-data/target/classes [INFO] [INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ adam-ibs-data --- [debug] execute contextualize [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/ikizema/DEV/PROJECTS/personal/adam-ibs-last/adam-ibs-data/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:2.3.2:testCompile (default-testCompile) @ adam-ibs-data --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.10:test (default-test) @ adam-ibs-data --- [INFO] No tests to run. [INFO] Surefire report directory: /home/ikizema/DEV/PROJECTS/personal/adam-ibs-last/adam-ibs-data/target/surefire-reports


T E S T S

Results :

Tests run: 0, Failures: 0, Errors: 0, Skipped: 0

[INFO] [INFO] --- maven-jar-plugin:2.3.2:jar (default-jar) @ adam-ibs-data --- [INFO] Building jar: /home/ikizema/DEV/PROJECTS/personal/adam-ibs-last/adam-ibs-data/target/adam-ibs-data-0.1.0.jar [INFO] [INFO] --- maven-install-plugin:2.3.1:install (default-install) @ adam-ibs-data --- [INFO] Installing /home/ikizema/DEV/PROJECTS/personal/adam-ibs-last/adam-ibs-data/target/adam-ibs-data-0.1.0.jar to /home/ikizema/.m2/repository/com/ets/mgl804/adam-ibs-data/0.1.0/adam-ibs-data-0.1.0.jar [INFO] Installing /home/ikizema/DEV/PROJECTS/personal/adam-ibs-last/adam-ibs-data/pom.xml to /home/ikizema/.m2/repository/com/ets/mgl804/adam-ibs-data/0.1.0/adam-ibs-data-0.1.0.pom [INFO]
[INFO] ------------------------------------------------------------------------ [INFO] Building Adam IBS Core 0.1.0 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ adam-ibs-core --- [INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ adam-ibs-core --- [debug] execute contextualize [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:2.3.2:compile (default-compile) @ adam-ibs-core --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scala-maven-plugin:3.1.3:compile (default) @ adam-ibs-core --- [WARNING] Expected all dependencies to require Scala version: 2.10.0 [WARNING] com.ets.mgl804:adam-ibs-data:0.1.0 requires scala version: 2.10.0 [WARNING] org.rogach:scallop_2.10:0.9.5 requires scala version: 2.10.3 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/ikizema/DEV/PROJECTS/personal/adam-ibs-last/adam-ibs-core/src/main/scala:-1: info: compiling [INFO] Compiling 16 source files to /home/ikizema/DEV/PROJECTS/personal/adam-ibs-last/adam-ibs-core/target/classes at 1446143723519 [INFO] No known dependencies. Compiling everything [WARNING] warning: there were 3 deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [INFO] prepare-compile in 0 s [INFO] compile in 11 s [INFO] [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ adam-ibs-core --- [debug] execute contextualize [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:2.3.2:compile (default-compile) @ adam-ibs-core --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scala-maven-plugin:3.1.3:compile (default) @ adam-ibs-core --- [WARNING] Expected all dependencies to require Scala version: 2.10.0 [WARNING] com.ets.mgl804:adam-ibs-data:0.1.0 requires scala version: 2.10.0 [WARNING] org.rogach:scallop_2.10:0.9.5 requires scala version: 2.10.3 [WARNING] Multiple versions of scala libraries detected! [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ adam-ibs-core --- [debug] execute contextualize [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/ikizema/DEV/PROJECTS/personal/adam-ibs-last/adam-ibs-core/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:2.3.2:testCompile (default-testCompile) @ adam-ibs-core --- [INFO] No sources to compile [INFO] [INFO] --- scala-maven-plugin:3.1.3:testCompile (default) @ adam-ibs-core --- [WARNING] Expected all dependencies to require Scala version: 2.10.0 [WARNING] com.ets.mgl804:adam-ibs-data:0.1.0 requires scala version: 2.10.0 [WARNING] org.rogach:scallop_2.10:0.9.5 requires scala version: 2.10.3 [WARNING] Multiple versions of scala libraries detected! [WARNING] No source files found. [INFO] [INFO] --- maven-surefire-plugin:2.13:test (default-test) @ adam-ibs-core --- [INFO] No tests to run. 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/home/ikizema/DEV/PROJECTS/personal/adam-ibs-last/adam-ibs-core/target/adam-ibs-core-0.1.0-jar-with-dependencies.jar to /home/ikizema/.m2/repository/com/ets/mgl804/adam-ibs-core/0.1.0/adam-ibs-core-0.1.0-jar-with-dependencies.jar [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] Adam IBS .......................................... SUCCESS [0.384s] [INFO] Adam IBS Data ..................................... SUCCESS [7.648s] [INFO] Adam IBS Core ..................................... SUCCESS [47.414s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 55.796s [INFO] Finished at: Thu Oct 29 14:36:08 EDT 2015 [INFO] Final Memory: 118M/1509M [INFO] ------------------------------------------------------------------------

Process finished with exit code 0

Je dépose le jar produit sur Gdrive et je ferme le ticket.

davidonlaptop commented 9 years ago

Quelle commande utilises-tu pour builder et dans quel repertoire es-tu?

davidonlaptop commented 9 years ago

As-tu essayé de rouler le .jar sur une option qui utilise spark ? Par exemple, "--make-bed".

iki-v commented 9 years ago

Oui, le jar doit être exécuté sur spark.

davidonlaptop commented 9 years ago

Est-ce que tu peux détailler ta procédure?

iki-v commented 9 years ago

J'ai mis un exemple d’exécution sur Spark 1.4.1 sur la page https://github.com/GELOG/adam-ibs. C'est dans "Execute from shell" puis "Execute with spark-submit".

Si tu le souhaite, je peux en mettre plus d'exemples. C'est également cette manière d’exécuter les jars qui est utilisé par Adam...