[toolbox] Galaxy wrappers and json description

.gitignore

@@ -19,4 +19,4 @@ met4j-core/src/main/java/fr/inra/toulouse/metexplore/met4j_core/Test\.java
 
 
 dependency-reduced-pom.xml
-/met4j.sif
+*.sif

.gitlab-ci.yml

@@ -3,6 +3,7 @@
 stages:
   - build
   - test
+  - package
   - deploy
   - build-containers
 
@@ -11,10 +12,34 @@ stages:
   image: docker:latest
   services:
     - docker:dind
+  script:
+    - if [ "$CI_COMMIT_BRANCH" = "master" ]; then docker build -t "$DOCKER_IMAGE:latest" .; fi
+    - if [ "$CI_COMMIT_BRANCH" = "master" ]; then docker push "$DOCKER_IMAGE:latest"; fi
+    - if [ "$CI_COMMIT_BRANCH" = "develop" -o "$CI_COMMIT_BRANCH" = "master" ]; then docker build -t "$DOCKER_IMAGE:$VERSION" .; fi
+    # version in lower case
+    - if [ "$CI_COMMIT_BRANCH" = "develop" -o "$CI_COMMIT_BRANCH" = "master" -a "$VERSION" != "$LOWER_CASE_VERSION" ]; then docker build -t "$DOCKER_IMAGE:$LOWER_CASE_VERSION" .; fi
+    - if [ "$CI_COMMIT_BRANCH" = "develop" -o "$CI_COMMIT_BRANCH" = "master" -a "$VERSION" != "$LOWER_CASE_VERSION" ]; then docker push "$DOCKER_IMAGE:$LOWER_CASE_VERSION"; fi
+    - docker build -t "$DOCKER_IMAGE:$CI_COMMIT_BRANCH" .
+    - docker push "$DOCKER_IMAGE:$CI_COMMIT_BRANCH"
+    # branch in lower case
+    - docker build -t "$DOCKER_IMAGE:$LOWER_CASE_COMMIT_BRANCH" .
+    - docker push "$DOCKER_IMAGE:$LOWER_CASE_COMMIT_BRANCH"
+  rules:
+    - if: $CI_COMMIT_BRANCH == "master"
+      when: always
+    - if: $CI_COMMIT_BRANCH == "develop"
+      when: always
+    - if: $CI_PIPELINE_SOURCE == "merge_request_event"
+      when: never
+    - if: $CI_COMMIT_BRANCH != $CI_DEFAULT_BRANCH
+      when: manual
+  needs:
+    - build
+    - package
 
 variables:
   MAVEN_CLI_OPTS: "-s .m2/settings.xml --batch-mode"
-  MAVEN_OPTS: "-Dmaven.repo.local=.m2/repository"
+  MAVEN_OPTS: "-Dmaven.repo.local=$CI_PROJECT_DIR/.m2/repository"
 
 cache:
   paths:
@@ -24,15 +49,45 @@ build:
   image: maven:3.6-adoptopenjdk-14
   stage: build
   script:
-    - mvn compile
+    - mvn $MAVEN_OPTS compile
+    - TRUEVERSION=$(mvn help:evaluate -Dexpression=project.version -q -DforceStdout)
+    - VERSION=$TRUEVERSION
+    - if [ "$CI_COMMIT_BRANCH" = "master" ]; then VERSION=${VERSION%"-SNAPSHOT"}; fi
+    - LOWER_CASE_VERSION=${VERSION,,}
+    - LOWER_CASE_COMMIT_BRANCH=${CI_COMMIT_BRANCH,,}
+    - echo "VERSION=$VERSION" >> build.env
+    - echo "TRUEVERSION=$TRUEVERSION" >> build.env
+    - echo "LOWER_CASE_VERSION=$LOWER_CASE_VERSION" >> build.env
+    - echo "LOWER_CASE_COMMIT_BRANCH=$LOWER_CASE_COMMIT_BRANCH" >> build.env
+  artifacts:
+    expire_in: 60 min
+    paths:
+      - target/
+      - "*/target"
+    reports:
+      dotenv: build.env
 
 test:
   image: maven:3.6-adoptopenjdk-14
   stage: test
   script:
-    - mvn clean test
+    - find . -name "*.class" -exec touch {} \+
+    - mvn $MAVEN_OPTS clean test
     - cat coverage/target/site/jacoco-aggregate/index.html | grep -o '<tfoot>.*</tfoot>'
 
+package:
+  image: maven:3.6-adoptopenjdk-14
+  stage: package
+  script:
+    - mvn $MAVEN_OPTS clean install -DskipTests=true
+    - cd met4j-toolbox
+    - mvn $MAVEN_OPTS package -DskipTests=true
+    - cd ..
+  artifacts:
+    expire_in: 60 min
+    paths:
+      - "met4j-toolbox/target/met4j-toolbox-$TRUEVERSION.jar"
+
 deploySnapshot:
   image: maven:3.6-adoptopenjdk-14
   stage: deploy
@@ -71,39 +126,35 @@ buildSingularity:
     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"
+    - if [ "$CI_COMMIT_BRANCH" = "master" ]; then singularity push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" met4j-toolbox.sif oras://"$CI_REGISTRY_IMAGE"/met4j-singularity:"latest"; fi
+    - if [ "$CI_COMMIT_BRANCH" = "develop" -o "$CI_COMMIT_BRANCH" = "master" ]; then singularity push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" met4j-toolbox.sif oras://"$CI_REGISTRY_IMAGE"/met4j-singularity:"$VERSION"; fi
+    # version in lower case
+    - if [ "$CI_COMMIT_BRANCH" = "develop" -o "$CI_COMMIT_BRANCH" = "master" -a "$VERSION" != "$LOWER_CASE_VERSION"]; then singularity push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" met4j-toolbox.sif oras://"$CI_REGISTRY_IMAGE"/met4j-singularity:"$LOWER_CASE_VERSION"; fi
+    - singularity push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" met4j-toolbox.sif oras://"$CI_REGISTRY_IMAGE"/met4j-singularity:"$CI_COMMIT_BRANCH"
+    # branch in lower case
+    - singularity push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" met4j-toolbox.sif oras://"$CI_REGISTRY_IMAGE"/met4j-singularity:"$LOWER_CASE_COMMIT_BRANCH"
   rules:
-    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
-      when: manual
+    - if: $CI_COMMIT_BRANCH == "master"
+      when: always
+    - if: $CI_COMMIT_BRANCH == "develop"
+      when: always
+    - if: $CI_PIPELINE_SOURCE == "merge_request_event"
+      when: never
     - if: $CI_COMMIT_BRANCH != $CI_DEFAULT_BRANCH
       when: manual
+  needs:
+    - build
+    - package
 
 buildDockerProdGitlab:
   extends: .template_docker
   before_script:
     - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
-  script:
-    - docker build -t "$CI_REGISTRY/metexplore/met4j/met4j-docker:latest" .
-    - docker push "$CI_REGISTRY/metexplore/met4j/met4j-docker:latest"
-  rules:
-    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
-      when: manual
-    - if: $CI_COMMIT_BRANCH != $CI_DEFAULT_BRANCH
-      when: manual
+    - DOCKER_IMAGE="$CI_REGISTRY/metexplore/met4j/met4j-docker"
+
 
 buildDockerProdDockerhub:
   extends: .template_docker
   before_script:
     - docker login -u "$DOCKERHUB_USER" -p "$DOCKERHUB_PASSWORD" $DOCKERHUB_REGISTRY
-  script:
-    - docker build --pull -t "$DOCKERHUB_IMAGE:latest" .
-    - docker push "$DOCKERHUB_IMAGE:latest"
-  rules:
-    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
-      when: manual
-    - if: $CI_COMMIT_BRANCH != $CI_DEFAULT_BRANCH
-      when: manual
-
-
-
-
+    - DOCKER_IMAGE=$DOCKERHUB_IMAGE
\ No newline at end of file

Dockerfile

@@ -4,25 +4,16 @@ RUN export DEBIAN_FRONTEND=noninteractive
 
 RUN apt-get update \
 && apt-get upgrade -y \
-&& apt-get install -y openjdk-11-jre git maven \
+&& apt-get install -y openjdk-11-jre maven \
 && apt-get clean \
 && apt-get purge
 
-RUN mkdir -p /opt && cd /opt \
-&& git clone https://forgemia.inra.fr/metexplore/met4j.git \
-&& cd met4j \
-&& mvn install \
-&& cd met4j-toolbox \
-&& mvn package
-
-RUN mkdir -p /opt/bin \
-&& cd /opt/met4j/met4j-toolbox \
-&& cp target/met4j*.jar /opt/bin/met4j.jar \
-&& cd /opt \
-&& rm -rf met4j ~/.m2  \
-&& apt-get remove -y git && apt-get autoremove -y
+RUN mkdir -p /opt/bin
 
 COPY ./docker_files/met4j.sh /opt/bin
+COPY ./met4j-toolbox/target/met4j*.jar /opt/bin/met4j.jar
+
+RUN chmod a+x /opt/bin/met4j.sh
 
-ENTRYPOINT ["/opt/bin/met4j.sh"]
+RUN cd /usr/bin && ln -s /opt/bin/met4j.sh
 

README.md

@@ -10,17 +10,14 @@
 **Met4J is an open-source Java library dedicated to the structural analysis of metabolic networks. It also came with a toolbox gathering CLI for several analyses relevant to metabolism-related research.**
 
 
-Met4j is composed by several modules:
+Met4j is composed by three main modules:
 - [met4j-core](met4j-core/README.md): it's the key module which contains all the core 
 classes for handling metabolic networks
 - [met4j-io](met4j-io/README.md): for importing/exporting metabolic networks in several 
 formats (SBML, MetExploreXml, KEGG)
 - [met4j-graph](met4j-graph/README.md): for performing graph-based topological analysis of metabolic networks.  
 
-The other modules contains utilities to serve the main modules listed here.  
-
-The full list of implemented metabolic network analysis can be found in the [met4j-toolbox](met4j-toolbox/README.md) 
-
+The package [met4j-toolbox](met4j-toolbox/README.md) contains high-level apps that can be run in command line by using either jar file or Singularity or Docker containers.
 
 
 ## Installation
@@ -52,41 +49,22 @@ git clone https://forgemia.inra.fr/metexplore/met4j.git;
 cd met4j;
 mvn clean install 
 ```
-to build the executable toolbox jar:
-```
-cd met4j-toolbox
-mvn clean compile assembly:single
-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 [here](https://forgemia.inra.fr/metexplore/tutorialmet4j).
 
-The toolbox can be launched using
-```
-java -jar met4j-toolbox-0.8.0-jar-with-dependencies.jar
-```
-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.  
 
 Please make sure to update tests as appropriate.  
 
+## Issues
+
+Issues or suggestions can be posted [here](https://forgemia.inra.fr/metexplore/met4j/-/issues).
+
 ## License
 Met4J is distributed under the open license [CeCILL-2.1](https://cecill.info/licences/Licence_CeCILL_V2.1-en.html) (compatible GNU-GPL).  
 

docker_files/met4j.sh

@@ -44,6 +44,6 @@ if [ $# -lt 1 ]
         echo "display Help"
         exec java -jar $path_jar
     else
-        echo "Lauch met4j-toolbox"
+        echo "Launch met4j-toolbox"
 	      exec java -Dlog4j.configuration= -cp $path_jar fr.inrae.toulouse.metexplore.met4j_toolbox."$@"
 fi
\ No newline at end of file

met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioEntity.java

@@ -81,7 +81,7 @@ public abstract class BioEntity {
      */
     public BioEntity(String id, String name) {
         if (StringUtils.isVoid(id)) {
-            String newId = UUID.randomUUID().toString().replaceAll("-", "_");
+            String newId = "_"+UUID.randomUUID().toString().replaceAll("-", "_");
             this.id = newId;
         } else {
             this.id = id;

met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/plugin/AnnotationParser.java

@@ -64,13 +64,15 @@ import static fr.inrae.toulouse.metexplore.met4j_core.utils.StringUtils.*;
  * because they do not extend the {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioPhysicalEntity} class
  *
  * @author Benjamin
- * @since 3.0
  * @version $Id: $Id
+ * @since 3.0
  */
 public class AnnotationParser implements PackageParser, AdditionalDataTag, ReaderSBML1Compatible, ReaderSBML2Compatible,
         ReaderSBML3Compatible {
 
-	/** Constant <code>ORIGIN="SBML"</code> */
+    /**
+     * Constant <code>ORIGIN="SBML"</code>
+     */
     public static final String ORIGIN = "SBML";
 
     /**
@@ -100,8 +102,7 @@ public class AnnotationParser implements PackageParser, AdditionalDataTag, Reade
     /**
      * Constructor
      *
-	 * @param useDefault
-	 *            true to use the {@link #defaultAnnotationPattern}
+     * @param useDefault true to use the {@link #defaultAnnotationPattern}
      */
     public AnnotationParser(boolean useDefault) {
         if (useDefault)
@@ -111,8 +112,7 @@ public class AnnotationParser implements PackageParser, AdditionalDataTag, Reade
     /**
      * Constructor
      *
-	 * @param pattern
-	 *            the user defined pattern
+     * @param pattern the user defined pattern
      */
     public AnnotationParser(String pattern) {
         this.annotationPattern = pattern;
@@ -127,14 +127,16 @@ public class AnnotationParser implements PackageParser, AdditionalDataTag, Reade
         return "annot";
     }
 
-	/** {@inheritDoc} */
+    /**
+     * {@inheritDoc}
+     */
     public boolean isPackageUseableOnModel(Model model) {
         return true;
     }
 
     /**
      * {@inheritDoc}
-	 *
+     * <p>
      * Parse all model entities to retrieve their annotations and extract the
      * desired information
      */
@@ -144,7 +146,7 @@ public class AnnotationParser implements PackageParser, AdditionalDataTag, Reade
         this.setBionetwork(bionetwork);
         this.setModel(model);
 
-		this.parseAnnotation(bionetwork,model.getAnnotation());
+        this.parseAnnotation(bionetwork, model.getAnnotation());
 
         this.parseSbmlAnnotations(bionetwork.getReactionsView());
         this.parseSbmlAnnotations(bionetwork.getMetabolitesView());
@@ -153,7 +155,6 @@ public class AnnotationParser implements PackageParser, AdditionalDataTag, Reade
     }
 
     /**
-	 * 
      * One of the different lists present in the {@link BioNetwork}
      * class
      */
@@ -163,8 +164,7 @@ public class AnnotationParser implements PackageParser, AdditionalDataTag, Reade
 
             String id = entry.getId();
 
-			if(entry.getAttribute("oldId") != null)
-			{
+            if (entry.getAttribute("oldId") != null) {
                 id = (String) entry.getAttribute("oldId");
             }
 
@@ -181,8 +181,7 @@ public class AnnotationParser implements PackageParser, AdditionalDataTag, Reade
     /**
      * Parse entity's annotation to extract external identifiers
      *
-	 * @param annot
-	 *            the SBML annotation element
+     * @param annot the SBML annotation element
      */
     private void parseAnnotation(BioEntity ent, Annotation annot) {
 
@@ -191,11 +190,10 @@ public class AnnotationParser implements PackageParser, AdditionalDataTag, Reade
 
             String qual;
 
-			if(cv.isBiologicalQualifier()) {
+            if (cv.isBiologicalQualifier()) {
 
                 qual = cv.getBiologicalQualifierType().getElementNameEquivalent();
-			}
-			else {
+            } else {
                 qual = cv.getModelQualifierType().getElementNameEquivalent();
             }
 
@@ -205,12 +203,10 @@ public class AnnotationParser implements PackageParser, AdditionalDataTag, Reade
 
                     if (m.group(1).equalsIgnoreCase("ec-code") && ent instanceof BioReaction) {
                         String oldEc = ((BioReaction) ent).getEcNumber();
-						if(isVoid(oldEc))
-						{
+                        if (isVoid(oldEc)) {
                             ((BioReaction) ent).setEcNumber(m.group(2));
-						}
-						else {
-							((BioReaction) ent).setEcNumber(oldEc+";"+m.group(2));
+                        } else {
+                            ((BioReaction) ent).setEcNumber(oldEc + ";" + m.group(2));
                         }
                     }
                     ent.addRef(m.group(1), m.group(2), 1, qual, ORIGIN);
@@ -221,17 +217,15 @@ public class AnnotationParser implements PackageParser, AdditionalDataTag, Reade
         String nonrdfAnnot = annot.getNonRDFannotationAsString();
         if (ent instanceof BioMetabolite && nonrdfAnnot != null && !nonrdfAnnot.isEmpty()) {
 
-			String specialInchiPattern = "<in:inchi xmlns:in=\"([^\"]+)\">InChI=([^<]+)</in:inchi>";
+            String specialInchiPattern = "InChI=([^<]+)";
 
             m = Pattern.compile(specialInchiPattern, Pattern.DOTALL).matcher(nonrdfAnnot);
 
             while (m.find()) {
-
-				if (m.group(1).equalsIgnoreCase("http://biomodels.net/inchi")) {
-					String inchi = m.group(2);
+                String inchi = m.group(1);
                 if (!ent.hasRef("inchi", inchi)) {
                     ent.addRef("inchi", inchi, 1, "is", ORIGIN);
-					}
+                    ((BioMetabolite) ent).setInchi(inchi);
                 }
             }
         }
@@ -249,8 +243,7 @@ public class AnnotationParser implements PackageParser, AdditionalDataTag, Reade
     /**
      * <p>Setter for the field <code>model</code>.</p>
      *
-	 * @param model
-	 *            the model to set
+     * @param model the model to set
      */
     public void setModel(Model model) {
         this.model = model;
@@ -268,8 +261,7 @@ public class AnnotationParser implements PackageParser, AdditionalDataTag, Reade
     /**
      * <p>Setter for the field <code>bionetwork</code>.</p>
      *
-	 * @param bionetwork
-	 *            the bionetwork to set
+     * @param bionetwork the bionetwork to set
      */
     public void setBionetwork(BioNetwork bionetwork) {
         this.bionetwork = bionetwork;
@@ -287,8 +279,7 @@ public class AnnotationParser implements PackageParser, AdditionalDataTag, Reade
     /**
      * <p>Setter for the field <code>annotationPattern</code>.</p>
      *
-	 * @param annotationPattern
-	 *            the annotationPattern to set
+     * @param annotationPattern the annotationPattern to set
      */
     public void setAnnotationPattern(String annotationPattern) {
         this.annotationPattern = annotationPattern;

met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/writer/plugin/AnnotationWriter.java

@@ -247,7 +247,7 @@ public class AnnotationWriter implements PackageWriter, AdditionalDataTag {
             addingLoop:
             for (BioRef r : refs) {
 
-                if (IdentifiersOrg.validIdentifiers.contains(r.getDbName().toLowerCase())){
+                if (IdentifiersOrg.validIdentifiers.contains(r.getDbName().toLowerCase()) && ! r.getDbName().equalsIgnoreCase("inchi")){
 
                     Qualifier qual;
 

met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetEcsFromFile.java

@@ -86,8 +86,6 @@ public class SetEcsFromFile extends AbstractSetAttributesFromFile {
 
         String[] ecs = ec.split(";");
 
-        System.err.println("ec : "+ec+" l :"+ecs.length);
-
         return Arrays.stream(ecs).allMatch(e -> {
             Matcher m = patternEC.matcher(e);
             return m.matches();

met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetRefsFromFile.java

@@ -101,7 +101,7 @@ public class SetRefsFromFile extends AbstractSetAttributesFromFile {
 
         int n = 0;
 
-        if(! IdentifiersOrg.validIdentifiers.contains(ref)) {
+        if(! IdentifiersOrg.validIdentifiers.contains(ref.toLowerCase())) {
             System.err.println("Warning : the identifier "+ref+" is not a valid id in identifiers.org");
         }
 

met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/plugin/AnnotationParserTest.java

@@ -260,6 +260,9 @@ public class AnnotationParserTest {
 
 		assertEquals(refInchis, s1.getRefs());
 
+		System.err.println(s1.getInchi());
+
+		assertEquals("truc", s1.getInchi());
 	}
 
 }

met4j-toolbox/README.md

 # met4j-toolbox
 **Met4j command-line toolbox for metabolic networks**
 
-## Installation
+## Installation from source
+
 ```
+git clone https://forgemia.inra.fr/metexplore/met4j.git;
+cd met4j;
+mvn clean install 
+
 cd met4j-toolbox
 mvn clean package
 ```
@@ -10,12 +15,120 @@ mvn clean package
 ## Usage
 The toolbox can be launched using
 ```
-java -jar met4j-toolbox-<version>.jar
+java -jar target/met4j-toolbox-<version>.jar
 ```
 which will list all the contained applications that can be called using
 
 ```
-java -cp met4j-toolbox-<version>.jar <Package>.<App name> -h
+java -cp target/met4j-toolbox-<version>.jar <Package>.<App name> -h
+```
+
+
+## From 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
+```
+
+If you want a specific version:
+
+```console
+singularity pull met4j-toolbox.sif oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:x.y.z
+```
+
+If you want the last develop version:
+
+```console
+singularity pull met4j-toolbox.sif oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop
+```
+
+If you want to build by yourself the singularity image:
+
+```console
+cd met4j-toolbox
+mvn package
+cd ../
+singularity build met4j-toolbox.sif met4j.singularity
+```
+
+
+This will download a singularity container met4j-toolbox.sif that you can directly launch.
+
+To list all the apps.
+```console
+met4j-toolbox.sif 
+```
+
+To launch a specific app, prefix its name with the last component of its package name. For instance:
+
+```console
+met4j-toolbox.sif convert.Tab2Sbml -h -in fic.tsv -sbml fic.sbml
+```
+
+By default, singularity does not see the directories that are not descendants of your home directory. To get the directories outside your home directory, you have to specify the SINGULARITY_BIND environment variable.
+At least, to get the data in the default reference directory, you have to specify:
+In bash:
+```console
+export SINGULARITY_BIND=/db
+```
+In csh or in tcsh
+```console
+setenv SINGULARITY_BIND /db
+```
+
+## From docker
+
+First install [Docker](https://www.docker.com/).
+
+Pull the latest met4j image:
+
+```console
+sudo docker pull metexplore/met4j:latest
+```
+
+If you want a specific version:
+
+```console
+sudo docker pull metexplore/met4j:x.y.z
+```
+
+If you want the develop version:
+```console
+sudo docker pull metexplore/met4j:develop
+```
+
+If you want to build by yourself the docker image:
+
+```console
+cd met4j-toolbox
+mvn package
+cd ../
+sudo docker build -t metexplore/met4j:myversion .
+```
+
+
+To list all the apps:
+```console
+sudo docker run metexplore/met4j:latest met4j.sh
+```
+
+Don't forget to map volumes when you want to process local files.
+Example:
+
+```console
+sudo docker run -v /home/lcottret/work:/work \
+ metexplore/met4j:latest met4j.sh convert.Sbml2Tab \
+ -in /work/toy_model.xml -out /work/toy_model.tsv
+```
+
+If you change the working directory, you have to specify "sh /usr/bin/met4j.sh":
+
+```console
+sudo docker run -w /work -v /home/lcottret/work:/work \