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vidjil
vidjil
Commits
74c7d926
Commit
74c7d926
authored
Oct 12, 2018
by
Mathieu Giraud
Browse files
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
Changes
5
Pipelines
1
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.gitlab-ci.yml
View file @
74c7d926
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@@ -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
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doc/server.md
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74c7d926
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@@ -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 t
he volume in the fuse volume block
`./vidjil/conf:/etc/vidjil`
.
This
will provide easier access to all of the
T
he volume
s
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
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docker/docker-compose.yml
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74c7d926
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@@ -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
:
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docker/vidjil-client/Dockerfile
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74c7d926
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@@ -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
...
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docker/vidjil-server/Dockerfile
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74c7d926
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@@ -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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