docker fix issues with docker images

fix fcgiwrap, imgt_proxy, cgi address in conf.js, add in cgi files. add
vidjil-algo

docker/vidjil-client/Dockerfile

@@ -4,7 +4,8 @@ label version="1.1"
 label description="An NGINX based docker image which comes \
 with a full installation of the Vidjil client."
 
-env GOSU_VERSION 1.7
+run sed -i 's/^\(user .*\)$/user www-data;/' /etc/nginx/nginx.conf
+
 run set -x \
 	&& apt-get update && apt-get install -y --no-install-recommends wget make unzip git sudo curl fcgiwrap && rm -rf /var/lib/apt/lists/*
 
@@ -21,6 +22,8 @@ copy ./conf/conf_http.js /opt/vidjil_conf/conf_http.js
 copy ./conf/nginx_web2py /opt/vidjil_conf/web2py
 copy ./conf/nginx_web2py_http /opt/vidjil_conf/web2py_http
 copy ./conf/Gemfile /usr/share/vidjil/Gemfile
+copy ./conf/align.cgi /usr/share/vidjil/browser/cgi/align.cgi
+copy ./conf/similarity.cgi /usr/share/vidjil/browser/cgi/similarity.cgi
 
 run cd /usr/share/vidjil/browser/css/icons && make
 run cd /usr/share/vidjil/germline && make

docker/vidjil-client/conf/conf.js

@@ -8,7 +8,7 @@ var config = {
     /* Used for the 'align' script 
      * If this is not defined, the 'align' button is not available
      */    
-    "cgi_address" : "http://localhost/cgi/", // Public test server
+    "cgi_address" : "https://localhost/cgi/", // Public test server
     // "cgi_address" : "http://127.0.1.1/cgi-bin/",
 
     /* The following options control how the user may have access to .vidjil files.

docker/vidjil-server/Dockerfile

@@ -13,8 +13,7 @@ run set -x \
 	&& gpg --keyserver ha.pool.sks-keyservers.net --recv-keys B42F6819007F00F88E364FD4036A9C25BF357DD4 \
 	&& gpg --batch --verify /usr/local/bin/gosu.asc /usr/local/bin/gosu \
 	&& rm -r "$GNUPGHOME" /usr/local/bin/gosu.asc \
-	&& chmod +x /usr/local/bin/gosu \
-	&& apt-get purge -y --auto-remove ca-certificates
+	&& chmod +x /usr/local/bin/gosu
 
 run apt-get update ; apt-get install --no-install-recommends --no-install-suggests -y -q sudo curl apt-utils uwsgi-plugin-python
 
@@ -38,6 +37,8 @@ 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
+
 copy ./scripts/uwsgi-entrypoint.sh /entrypoints/uwsgi-entrypoint.sh
 copy ./scripts/fuse-entrypoint.sh /entrypoints/fuse-entrypoint.sh
 run mkdir /usr/share/vidjil/server/web2py/applications/vidjil/databases && touch /usr/share/vidjil/server/web2py/applications/vidjil/databases/sql.log

docker/vidjil-server/conf/defs.py

@@ -37,7 +37,7 @@ BASENAME_OUT_VIDJIL_ID = '%06d'
 
 ### Directory for program used in task.py
 ### relative path start from server/web2py
-DIR_VIDJIL = '/usr/bin/'
+DIR_VIDJIL = '/usr/share/vidjil/'
 DIR_FUSE = '../../tools'
 DIR_MIXCR = '/usr/bin'
 DIR_IGREC = '/usr/local/bin/'

docker/vidjil-server/conf/defs_http.py

@@ -37,7 +37,7 @@ BASENAME_OUT_VIDJIL_ID = '%06d'
 
 ### Directory for program used in task.py
 ### relative path start from server/web2py
-DIR_VIDJIL = '/usr/bin/'
+DIR_VIDJIL = '/usr/share/vidjil/'
 DIR_FUSE = '../../tools'
 DIR_MIXCR = '/usr/bin'
 DIR_IGREC = '/usr/local/bin/'