Commit 74c7d926 authored by Mathieu Giraud's avatar Mathieu Giraud

Merge branch 'docker_germline_js' into 'dev'

Gestion des germlines et config dans docker

Closes #3521

See merge request !317
parents f4125f01 fb7dee10
Pipeline #43954 canceled with stages
......@@ -297,6 +297,7 @@ test_server_functional:
- docker build --no-cache --build-arg git_branch=$CI_COMMIT_REF_NAME --build-arg build_env=TEST -t "vidjil/client:test" docker/vidjil-client
- sed -i '/\/etc\/nginx\/ssl\:\/etc\/nginx\/ssl/d' ./docker/docker-compose.yml
- sed -i 's/\:latest/\:test/g' ./docker/docker-compose.yml
- make germline && cp browser/js/germline.js docker/vidjil-client/conf
- cd docker && docker-compose up -d && cd ..
- sed -i "s/^python\ \.\.\/\.\.\/\.\./docker\ exec\ docker_uwsgi_1\ python\ \/usr\/share\/vidjil\/server\/web2py/" server/web2py/applications/vidjil/tests/init_func_test_db.sh
- docker exec docker_uwsgi_1 sed -i "s/^\(FILE_SOURCE .*\)/FILE_SOURCE = '\/usr\/share\/vidjil\/demo'/" /usr/share/vidjil/server/web2py/applications/vidjil/modules/defs.py
......
......@@ -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
......
......@@ -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:
......
......@@ -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
......
......@@ -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
......
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