diff --git a/docker/vidjil-client/Dockerfile b/docker/vidjil-client/Dockerfile index b2259a4cdb53d76e2a68eabd0eba33c4513e23bc..c28f4d06ea944cdb1548aaa048c0763771f7548a 100644 --- a/docker/vidjil-client/Dockerfile +++ b/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 diff --git a/docker/vidjil-client/conf/align.cgi b/docker/vidjil-client/conf/align.cgi new file mode 100755 index 0000000000000000000000000000000000000000..8645d7faab42a04c020c1cab7fd3d1ddbc5a22a1 Binary files /dev/null and b/docker/vidjil-client/conf/align.cgi differ diff --git a/docker/vidjil-client/conf/conf.js b/docker/vidjil-client/conf/conf.js index be206f325da9cc7559c8b913d7a0b472919b15bf..42d93e5f79bedbdf8020f49fad8ca17e9fe2d41c 100644 --- a/docker/vidjil-client/conf/conf.js +++ b/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. diff --git a/docker/vidjil-client/conf/similarity.cgi b/docker/vidjil-client/conf/similarity.cgi new file mode 100755 index 0000000000000000000000000000000000000000..7fc916e34f514b00858282f83f0146112aa1343f Binary files /dev/null and b/docker/vidjil-client/conf/similarity.cgi differ diff --git a/docker/vidjil-server/Dockerfile b/docker/vidjil-server/Dockerfile index e4bb1c94d47942c78ce1643e235e69fc8a3040d9..1445b0672a6094e5fc6fe96c6da931c2ba41ad2c 100644 --- a/docker/vidjil-server/Dockerfile +++ b/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 diff --git a/docker/vidjil-server/conf/defs.py b/docker/vidjil-server/conf/defs.py index 8b023fee28e6c59c32bb896b51b0204199febb15..1928488562d876a3531cb4a1fa16506df28e1306 100644 --- a/docker/vidjil-server/conf/defs.py +++ b/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/' diff --git a/docker/vidjil-server/conf/defs_http.py b/docker/vidjil-server/conf/defs_http.py index 6269bc5cd6c2b1a0cbd271c722fc0743a313bbe9..928436f565d61f5e4d27f0ec8c6f5f66c50a5ced 100644 --- a/docker/vidjil-server/conf/defs_http.py +++ b/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/'