fix docker

Dockerfile

 FROM eclipse-temurin:17-jdk-alpine
 
-RUN apk update && apk add maven
+RUN apk update && apk add bash
 
-RUN mkdir -p /opt/bin
+RUN mkdir /opt/bin
 
-COPY ./docker_files/met4j.sh /opt/bin
+COPY ./docker_files/met4j.sh /opt/bin/met4j.sh
 COPY ./met4j-toolbox/target/met4j*.jar /opt/bin/met4j.jar
 
-RUN chmod a+x /opt/bin/met4j.sh
+RUN chmod 755 /opt/bin/met4j.sh
 
-RUN cd /usr/bin && ln -s /opt/bin/met4j.sh
+RUN ln -s /opt/bin/met4j.sh /usr/bin/met4j.sh
+
+#ENTRYPOINT ["/opt/bin/met4j.sh"]
+ENTRYPOINT ["bash", "/opt/bin/met4j.sh"]
 

met4j-toolbox/README.md

@@ -111,6 +111,7 @@ sudo docker pull metexplore/met4j:develop
 If you want to build by yourself the docker image:
 
 ```console
+mvn clean install
 cd met4j-toolbox
 mvn package
 cd ../
@@ -120,24 +121,24 @@ sudo docker build -t metexplore/met4j:myversion .
 
 To list all the apps:
 ```console
-sudo docker run metexplore/met4j:latest met4j.sh
+sudo docker run metexplore/met4j:latest
 ```
 
-Don't forget to map volumes when you want to process local files.
-Example:
+To run an app, you have to specify the full name of the app, 
+with the last part of the package name and the app name separated by a dot.
+For instance:
 
 ```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
+sudo docker run metexplore/met4j:latest convert.Tab2Sbml -h
 ```
 
-If you change the working directory, you have to specify "sh /usr/bin/met4j.sh":
+Don't forget to map volumes when you want to process local files.
+Example:
 
 ```console
-sudo docker run -w /work -v /home/lcottret/work:/work \
- metexplore/met4j:latest sh /usr/bin/met4j.sh convert.Sbml2Tab \
- -in toy_model.xml -out toy_model.tsv
+sudo docker run -v /home/lcottret/work:/work \
+ metexplore/met4j:latest convert.Sbml2Tab \
+ -in /work/toy_model.xml -out /work/toy_model.tsv
 ```
 
 ### Galaxy instance