Merge branch 'singularity' into 'develop'

Singularity

See merge request !12

.gitlab-ci.yml

-image: maven:3.6-adoptopenjdk-14
+
+
+stages:
+  - build
+  - test
+  - deploy
+  - singularity
 
 variables:
   MAVEN_CLI_OPTS: "-s .m2/settings.xml --batch-mode"
@@ -9,17 +15,20 @@ cache:
     - .m2/repository/
 
 build:
+  image: maven:3.6-adoptopenjdk-14
   stage: build
   script:
     - mvn compile
 
 test:
+  image: maven:3.6-adoptopenjdk-14
   stage: test
   script:
     - mvn clean test
     - cat coverage/target/site/jacoco-aggregate/index.html | grep -o '<tfoot>.*</tfoot>'
 
 deploySnapshot:
+  image: maven:3.6-adoptopenjdk-14
   stage: deploy
   script:
     - mvn $MAVEN_CLI_OPTS deploy -Dmaven.test.skip=true
@@ -27,6 +36,7 @@ deploySnapshot:
     - develop
 
 deployCentral:
+  image: maven:3.6-adoptopenjdk-14
   stage: deploy
   before_script:
     - 'which ssh-agent || ( apt-get update -qy && apt-get install openssh-client -qqy )'
@@ -47,3 +57,14 @@ deployCentral:
     - mvn $MAVEN_CLI_OPTS release:perform -Darguments=-Dgpg.passphrase=${GPG_PASSPHRASE} -DlocalCheckout=true
   only:
     - master
+
+buildSingularity:
+  stage: singularity
+  image:
+    name: quay.io/singularity/singularity:v3.4.0
+    entrypoint: [ "" ]
+  script:
+    - singularity build met4j-toolbox.sif met4j.singularity
+    - singularity push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" met4j-toolbox.sif oras://"$CI_REGISTRY_IMAGE"/met4j-singularity:"$CI_COMMIT_TAG"
+  when: manual
+

README.md

@@ -62,7 +62,7 @@ mv ./target/*-jar-with-dependencies.jar ../../../
 ## Usage
 
 Documentation for the library modules can be found in each module's own README.  
-Detailed code examples can be found at [https://forgemia.inra.fr/metexplore/tutorialmet4j](https://cecill.info/licences/Licence_CeCILL_V2.1-en.html).  
+Detailed code examples can be found at [here](https://forgemia.inra.fr/metexplore/tutorialmet4j).  
 
 The toolbox can be launched using
 ```
@@ -74,6 +74,14 @@ which will list all the contained applications that can be called using
 java -cp met4j-toolbox-0.8.0-jar-with-dependencies.jar <App full name> -h
 ```
 
+### With singularity
+
+You need at least [singularity](https://sylabs.io/guides/3.5/user-guide/quick_start.html) v3.5.
+
+```console
+singularity pull met4j-toolbox.sif oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:latest
+```
+
 ## Contributing
 Pull requests are welcome **on the gitlab repo** ([https://forgemia.inra.fr/metexplore/met4j](https://forgemia.inra.fr/metexplore/met4j)). For major changes, please open an issue first to discuss what you would like to change.  
 

met4j.singularity

+Bootstrap: docker
+From: debian:stable-slim
+
+%runscript
+    if [ $# -lt 1 ] 
+    then
+        echo "display Help"
+        exec java -jar /opt/bin/met4j.jar
+    else
+        echo "Lauch met4j-toolbox"
+	    exec java -Dlog4j.configuration= -cp /opt/bin/met4j.jar fr.inrae.toulouse.metexplore.met4j_toolbox."$@"
+    fi
+
+%help
+
+Usage: met4j.sif
+
+This is singularity container for met4j
+
+
+
+%labels
+    Maintainer Ludovic.Cottret@inrae.fr
+    
+%post
+    export DEBIAN_FRONTEND=noninteractive
+	apt-get update && \
+    apt-get upgrade -y && \
+    apt-get install -y \
+        openjdk-11-jre   \
+        git \
+        maven
+    apt-get clean && \
+    apt-get purge 
+
+	mkdir -p /opt
+
+    cd /opt
+
+    git clone https://forgemia.inra.fr/metexplore/met4j.git
+
+    cd met4j/
+    
+    mvn install
+
+    cd met4j-toolbox
+
+    mvn package
+
+    mkdir -p /opt/bin
+
+    cp target/met4j*.jar /opt/bin/met4j.jar
+
+    cd /opt 
+
+    rm -rf met4j ~/.m2
+
+    apt-get remove -y maven git
+
+    apt-get autoremove -y
+
+%environment
+    export LC_ALL=C