server.md docker/* better gemline management

Ensure germlines aren't packaged in the server image. Use volumes and
symlinks so that it is no longer necessary to alter containers to add
germlines.

See #3521

doc/server.md

@@ -233,13 +233,28 @@ vidjil image you want to use. Usually this will be `vidjil/vidjil:latest`,
 but more tags are available at <https://hub.docker.com/r/vidjil/vidjil/tags/>.
 
 XXXX ? XXXX
-You may also want to uncomment the volume in the fuse volume block 
-`./vidjil/conf:/etc/vidjil`.
-This will provide easier access to all of the
+The volumes in the fuse and nginx volume block
+`./vidjil-server/conf:/etc/vidjil` and `./vidjil-client/conf:/etc/vidjil`
+will provide easier access to all of the
 configuration files, allowing for tweaks.
 From this location, it will be easier to enable more software or pipelines
 by putting their binaries in this location taht will be see by the docker instance.
 
+# Docker -- Gerlmines
+
+In order to use Vidjil, you will need to retrieve the germline files.
+
+From the root of the git repository run:
+```sh
+cd gerlmine
+make
+```
+These germlines are included in the server container with a volume in the fuse block
+in your `docker-compose.yml`: `../germline:/usr/share/vidjil/germline`.
+
+After retrieving the germlines, you will also need to copy the generated `germline.js`
+(found in `browser/js/`) into the `docker/vidjil-client/conf` directory.
+
 
 # Docker -- Troubleshooting
 

docker/docker-compose.yml

@@ -29,7 +29,8 @@ services:
             - /opt/vidjil/log:/var/vidjil
             - /opt/vidjil/log/uwsgi:/var/log/uwsgi
             - /opt/vidjil/backup:/mnt/backup
-            #- ./vidjil-server/conf:/etc/vidjil
+            - ./vidjil-server/conf:/etc/vidjil
+            - ../germline:/usr/share/vidjil/germline
     nginx:
         image: vidjil/client:latest
         depends_on:
@@ -43,6 +44,7 @@ services:
         volumes:
             - /opt/vidjil/log/nginx:/var/log/nginx
             - /etc/nginx/ssl:/etc/nginx/ssl
+            - ./vidjil-client/conf:/etc/vidjil
             - ../germline:/usr/share/vidjil/germline
 
     workers:

docker/vidjil-client/Dockerfile

@@ -34,6 +34,7 @@ run mkdir /etc/vidjil
 run rm /etc/nginx/conf.d/default.conf
 run chmod +x /opt/install_scripts/install.sh; sync && /opt/install_scripts/install.sh
 run ln -s /etc/vidjil/conf.js /usr/share/vidjil/browser/js/conf.js
+run ln -s /etc/vidjil/germline.js /usr/share/vidjil/browser/js/germline.js
 
 copy ./scripts/nginx-entrypoint.sh /entrypoints/nginx-entrypoint.sh
 run chown -R www-data:www-data /usr/share/vidjil

docker/vidjil-server/Dockerfile

@@ -37,7 +37,7 @@ run chmod +x /opt/install_scripts/install.sh; sync && /opt/install_scripts/insta
 run ln -s /etc/vidjil/defs.py /usr/share/vidjil/server/web2py/applications/vidjil/modules/defs.py
 run ln -s /etc/vidjil/wsgihandler.py /usr/share/vidjil/server/web2py/wsgihandler.py
 
-run wget http://www.vidjil.org/releases/vidjil-latest_x86_64 && mv vidjil-latest_x86_64 /usr/share/vidjil/vidjil-algo && cd /usr/share/vidjil/ && chmod +x vidjil-algo && cd germline && make
+run wget http://www.vidjil.org/releases/vidjil-latest_x86_64 && mv vidjil-latest_x86_64 /usr/share/vidjil/vidjil-algo && cd /usr/share/vidjil/ && chmod +x vidjil-algo
 
 copy ./scripts/uwsgi-entrypoint.sh /entrypoints/uwsgi-entrypoint.sh
 copy ./scripts/fuse-entrypoint.sh /entrypoints/fuse-entrypoint.sh