examind_conf_cwl.md

title	Configure Examind for CWL Processes

To run CWL processes in Examind, you need to configure and edit some configuration files, Docker images, and docker compose files.

A. Dockerfile of Examind-Community

First we need to install cwltool and cwl-runner inside the Examind-Community Docker image.

The Dockerfile is located in this folder in the Examind Community repository: examind-community/modules/bundles/exa-bundle/src/docker

# previous content of the Dockerfile
# > LABEL description="Docker image of Examind Community"

# Lines to add
RUN apt-get update && \
    apt-get install -y python3 python3-pip docker.io && \
    rm -rf /var/lib/apt/lists/*

RUN pip3 install --no-cache-dir cwltool --break-system-packages && \
    pip3 install --no-cache-dir cwlref-runner --break-system-packages

# next content of the Dockerfile
# > COPY ./examind /usr/local/tomcat/webapps/examind

B. Edit setenv.sh

Next we need to edit the setenv.sh

The setenv.sh is located in this folder in the Examind Community repository: examind-community/modules/bundles/exa-bundle/src/docker/conf/tomcat/bin

Add this at the end of the file setenv.sh:

JAVA_OPTS="${JAVA_OPTS} --add-opens java.base/java.net=ALL-UNNAMED"
export JAVA_OPTS

C. Edit the docker-compose.yml

Finally, we need to edit the docker-compose.yml file.

The docker-compose is located in this folder in the Examind Community repository: /examind-community/docker

If you are using docker in root mode, you can add the following volume to the examind service:

    volumes:
       - "/var/run/docker.sock:/var/run/docker.sock"
       - "/usr/bin/docker:/usr/bin/docker"

If you are using podman in rootless mode , you can add the following volume to the examind service (cf : Podman Rootless Conf):

    volumes:
         - "/run/user/<num_user>/podman/podman.sock:/var/run/docker.sock"

Replace <num_user> by your user id (you can get it by running the command id -u in a terminal)

---

Always in the volume section you have to add a volume for the CWL processes. This volume have to point a folder with the same path inside and outside the container. Example for me :

    volumes:
       - "/home/qbialota/.local/share/exa-cwl-shared:/home/qbialota/.local/share/exa-cwl-shared"

Warning : If you are on SELinux system (like Fedora, CentOS, RHEL...), you have to add the option :z at the end of the volume path to avoid permission issues. Example for me on SELinux system :

    volumes:
       - "/home/qbialota/.local/share/exa-cwl-shared:/home/qbialota/.local/share/exa-cwl-shared:Z"
       - "/run/user/<num_user>/podman/podman.sock:/var/run/docker.sock:Z"

---

Finaly you have to set an environment variable with the same path as the volume for CWL processes. Example for me :

  EXAMIND_CWL_SHARED_DIR: "/home/qbialota/.local/share/exa-cwl-shared"

D. Build examind-community

To build examind-community with the modified Dockerfile, you have to run the following command at the root of the examind-community repository:

mvn install -DskipTests -Pdocker -f pom.xml