ssh -YX root@147.99.108.172 docker run -i -t -p 8090:90 bgruening/galaxy-stable /bin/bash Instaler ipython : git clone https://github.com/bgruening/galaxy-ipython.git config/plugins/visualizations/ipython ou git clone https://github.com/bgruening/galaxy-ipython.git /root/sarah/docker-galaxy-stable/config/plugins/visualizations/ipython Le fichier utilisé par défaut : config/galaxy.ini.sample Avec : port : 8080 --> port=8090 host : 127.0.0.1 puis lancement de Galaxy: sh run.sh & Once Galaxy completes startup, you should be able to view Galaxy in your browser at: http://localhost:8080 --> NOK OperationalError: (psycopg2.OperationalError) could not connect to server: Connection refused Is the server running on host "localhost" (::1) and accepting TCP/IP connections on port 5432? could not connect to server: Connection refused Is the server running on host "localhost" (127.0.0.1) and accepting TCP/IP connections on port 5432? ^C [1]+ Exit 1 sh run.sh Check process sur un autre terminal: ssh -YX root@147.99.108.172 [root@vm-docker-test docker-galaxy-stable]# ps aux | grep galaxy root 2817 0.0 0.0 361156 11696 pts/0 Sl+ 17:01 0:00 /usr/bin/docker-current run -i -t -p 8080:80 bgruening/galaxy-stable /bin/bash root 3047 0.0 0.0 112664 952 pts/2 S+ 17:14 0:00 grep --color=auto galaxy METHODE 2: docker run -d -p 8080:80 -p 8021:21 -p 8022:22 bgruening/galaxy-stable [root@vm-docker-test docker-galaxy-stable]# ps aux | grep galaxy 1450 3618 18.6 0.2 468768 185692 ? S 17:39 0:08 /galaxy_venv/bin/python /galaxy_venv/bin/uwsgi --virtualenv /galaxy_venv --ini-paste /etc/galaxy/galaxy.ini --logdate --master --processes 2 --threads 4 --logto /home/galaxy/logs/uwsgi.log --socket 127.0.0.1:4001 --pythonpath lib --stats 127.0.0.1:9191 1450 3638 16.2 0.2 1482720 172184 ? Sl 17:39 0:06 /galaxy_venv/bin/python ./lib/galaxy/main.py -c /etc/galaxy/galaxy.ini --server-name=handler0 --log-file=/home/galaxy/logs/handler0.log 1450 3639 16.2 0.2 1482720 170052 ? Sl 17:39 0:06 /galaxy_venv/bin/python ./lib/galaxy/main.py -c /etc/galaxy/galaxy.ini --server-name=handler1 --log-file=/home/galaxy/logs/handler1.log 1450 3670 11.4 0.1 1106740 113740 ? Sl 17:39 0:04 /galaxy_venv/bin/python ./scripts/paster.py serve /etc/galaxy/reports_wsgi.ini --server-name=main --pid-file=/home/galaxy/logs/reports.pid --log-file=/home/galaxy/logs/reports.log 1450 3706 2.3 0.0 838060 18176 ? Sl 17:40 0:00 node /galaxy-central/lib/galaxy/web/proxy/js/lib/main.js --sessions database/session_map.sqlite --ip 0.0.0.0 --port 8800 1450 3788 0.1 0.0 322796 5732 ? Sl 17:40 0:00 /usr/sbin/slurmctld -L /home/galaxy/logs/slurmctld.log root 3791 0.0 0.0 111800 1700 ? S 17:40 0:00 /usr/sbin/slurmd -L /home/galaxy/logs/slurmd.log 1550 3814 0.1 0.0 248740 9164 ? Ss 17:40 0:00 postgres: galaxy galaxy ::1(42538) idle 1550 3815 0.1 0.0 248740 9004 ? Ss 17:40 0:00 postgres: galaxy galaxy ::1(42539) idle root 3821 0.2 0.0 5968 624 ? S 17:40 0:00 tail -f /home/galaxy/logs/handler0.log /home/galaxy/logs/handler1.log /home/galaxy/logs/reports.log /home/galaxy/logs/slurmctld.log /home/galaxy/logs/slurmd.log /home/galaxy/logs/uwsgi.log 1550 3853 0.0 0.0 247952 7008 ? Ss 17:40 0:00 postgres: galaxy galaxy ::1(42545) idle 1550 3855 0.6 0.0 248732 8708 ? Ss 17:40 0:00 postgres: galaxy galaxy ::1(42546) idle 1550 3858 0.4 0.0 248436 9156 ? Ss 17:40 0:00 postgres: galaxy galaxy ::1(42547) idle 1550 3868 0.0 0.0 247952 6976 ? Ss 17:40 0:00 postgres: galaxy galaxy ::1(42548) idle 1550 3870 0.6 0.0 248736 8716 ? Ss 17:40 0:00 postgres: galaxy galaxy ::1(42549) idle 1550 3871 0.2 0.0 248436 7744 ? Ss 17:40 0:00 postgres: galaxy galaxy ::1(42550) idle 1450 3873 2.0 0.2 911160 181092 ? Sl 17:40 0:00 /galaxy_venv/bin/python /galaxy_venv/bin/uwsgi --virtualenv /galaxy_venv --ini-paste /etc/galaxy/galaxy.ini --logdate --master --processes 2 --threads 4 --logto /home/galaxy/logs/uwsgi.log --socket 127.0.0.1:4001 --pythonpath lib --stats 127.0.0.1:9191 1450 3876 2.0 0.2 911160 181092 ? Sl 17:40 0:00 /galaxy_venv/bin/python /galaxy_venv/bin/uwsgi --virtualenv /galaxy_venv --ini-paste /etc/galaxy/galaxy.ini --logdate --master --processes 2 --threads 4 --logto /home/galaxy/logs/uwsgi.log --socket 127.0.0.1:4001 --pythonpath lib --stats 127.0.0.1:9191 1550 3887 0.2 0.0 248436 7744 ? Ss 17:40 0:00 postgres: galaxy galaxy ::1(42551) idle 1550 3888 0.2 0.0 248436 7736 ? Ss 17:40 0:00 postgres: galaxy galaxy ::1(42552) idle root 3905 0.0 0.0 112668 952 pts/2 S+ 17:40 0:00 grep --color=auto galaxy *************************************************************************************************************************************************** *************************************************************************************************************************************************** *************************************************************************************************************************************************** [root@vm-docker-test docker-galaxy-stable]# ls compose/galaxy-proftpd/run.sh compose/galaxy-proftpd/run.sh [root@vm-docker-test docker-galaxy-stable]# sh /compose/galaxy-proftpd/run.sh & [root@vm-docker-test docker-galaxy-stable]# compose/galaxy-proftpd/run.sh: ligne28: ansible-playbook : commande introuvable compose/galaxy-proftpd/run.sh: ligne31: proftpd : commande introuvable *************************************************************************************************************************************************** *************************************************************************************************************************************************** *************************************************************************************************************************************************** tu pourras refaire des tests et me dire si cela fonctionne maintenant (il manque http, quelques paquets pour le graphique etc. En tout cas de mon côté ça fonctionne quand je fais: docker run -d -p 8080:80 -p 8021:21 -p 8022:22 bgruening/galaxy-stable puis sur la machine vm-docker-test firefox & et connexion sur http://localhost:8080 --> Mails il n'y a pas ipython Install de iPython: git clone https://github.com/bgruening/galaxy-ipython.git config/plugins/visualizations/ipython [root@vm-docker-test config]# pwd /root/sarah/docker-galaxy-stable/config Ajout chemin dans galaxy.ini: pas de galaxy.ini !!! *************************************************************************************************************************************************** *************************************************************************************************************************************************** *************************************************************************************************************************************************** 1 - Install de Galaxy sur une machine Docker: [root@vm-docker-test sarah]# git clone -b release_17.05 https://github.com/galaxyproject/galaxy.git Cloning into 'galaxy'... remote: Counting objects: 279430, done. remote: Compressing objects: 100% (14/14), done. [root@vm-docker-test sarah]# ls docker-galaxy-stable galaxy [root@vm-docker-test sarah]# cd galaxy/ [root@vm-docker-test galaxy]# ls CITATION contrib cron external_service_types locale openid run_reports.sh scripts test tools client CONTRIBUTING.md database extract_dataset_parts.sh Makefile README.rst run.sh setup.cfg test-data tox.ini CODE_OF_CONDUCT.md CONTRIBUTORS.md display_applications lib manage_db.sh requirements.txt run_tests.sh static tool-data config create_db.sh doc LICENSE.txt manage_tools.sh rolling_restart.sh run_tool_shed.sh templates tool_list.py [root@vm-docker-test galaxy]# cp config/galaxy.ini.sample config/galaxy.ini [root@vm-docker-test galaxy]# geany config/galaxy.ini & --> port=8090 (au lieu de 8080) [root@vm-docker-test galaxy]# sh run.sh Initializing config/migrated_tools_conf.xml from migrated_tools_conf.xml.sample Initializing config/shed_tool_conf.xml from shed_tool_conf.xml.sample Initializing config/shed_tool_data_table_conf.xml from shed_tool_data_table_conf.xml.sample Initializing config/shed_data_manager_conf.xml from shed_data_manager_conf.xml.sample Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample Initializing static/welcome.html from welcome.html.sample Fetching https://pypi.python.org/packages/source/v/virtualenv/virtualenv-13.1.2.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed .................... Starting server in PID 9547. serving on http://127.0.0.1:8090 sur le terminal de vm-docker-test firefox & Puis ouvrir http://127.0.0.1:8090 --> Galaxy OK 2- Install de iPython: git clone https://github.com/bgruening/galaxy-ipython.git config/plugins/visualizations/ipython [root@vm-docker-test galaxy]# git clone https://github.com/bgruening/galaxy-ipython.git config/plugins/visualizations/ipython Cloning into 'config/plugins/visualizations/ipython'... remote: Counting objects: 683, done. remote: Total 683 (delta 0), reused 0 (delta 0), pack-reused 683 Receiving objects: 100% (683/683), 311.62 KiB | 0 bytes/s, done. Resolving deltas: 100% (335/335), done. 3 - Relancer Galaxy: ./run.sh Pas d'icône "visualisation": Ajout d'un paramètre dans galaxy.ini : # Interactive environment plugins root directory: where to look for interactive # environment plugins. By default none will be loaded. Set to # config/plugins/interactive_environments to load Galaxy's stock plugins # (currently just Jupyter). These will require Docker to be configured and # have security considerations, so proceed with caution. The path is relative to the # Galaxy root dir. To use an absolute path begin the path with '/'. This is a comma # separated list. #interactive_environment_plugins_directory =config/plugins/interactive_environments galaxy.web.base.pluginframework INFO 2017-08-03 12:58:43,865 VisualizationsRegistry, loaded plugin: charts galaxy.visualization.plugins.config_parser INFO 2017-08-03 12:58:43,867 Visualizations plugin disabled: Circster. Skipping... galaxy.visualization.plugins.config_parser INFO 2017-08-03 12:58:43,869 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2017-08-03 12:58:43,870 VisualizationsRegistry, loaded plugin: csg galaxy.visualization.plugins.config_parser INFO 2017-08-03 12:58:43,872 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2017-08-03 12:58:43,873 VisualizationsRegistry, loaded plugin: graphviz galaxy.visualization.plugins.config_parser INFO 2017-08-03 12:58:43,874 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2017-08-03 12:58:43,875 VisualizationsRegistry, loaded plugin: ipython galaxy.web.base.pluginframework INFO 2017-08-03 12:58:43,878 VisualizationsRegistry, loaded plugin: phyloviz galaxy.web.base.pluginframework INFO 2017-08-03 12:58:43,880 VisualizationsRegistry, loaded plugin: scatterplot galaxy.visualization.plugins.config_parser INFO 2017-08-03 12:58:43,882 Visualizations plugin disabled: Sweepster. Skipping... galaxy.web.base.pluginframework INFO 2017-08-03 12:58:43,884 VisualizationsRegistry, loaded plugin: trackster Solution : https://galaxyproject.org/visualizations-registry/ Je vais enlever ceux qui n'arrivent pas à charger : Circster et Sweepster [root@vm-docker-test galaxy]# ls config/plugins/visualizations/ additional_template_paths.xml charts circster common csg graphviz ipython phyloviz README.txt scatterplot sweepster trackster visualization.dtd [root@vm-docker-test galaxy]# cd config/plugins/visualizations/ [root@vm-docker-test visualizations]# mv circster /root/sarah/. [root@vm-docker-test visualizations]# mv sweepster /root/sarah/. [root@vm-docker-test visualizations]# ls additional_template_paths.xml charts common csg graphviz ipython phyloviz README.txt scatterplot trackster visualization.dtd Start Galaxy : ./run.sh *************************************************************************************************************************************************** *************************************************************************************************************************************************** *************************************************************************************************************************************************** A partir du code Galaxy v 17 récupéré. Créer un Dockerfile: [root@vm-docker-test galaxy]# more Dockerfile # Galaxy - Docker # # VERSION Galaxy-central FROM toolshed/requirements MAINTAINER Sarah Maman RUN sh /root/sarah/galaxy/run.sh & Attention, port = 8090 (dans galaxy.ini file) construction du galaxy sous Docker: [root@vm-docker-test galaxy]# docker build -t galaxy-docker-sarah . Sending build context to Docker daemon 621.7 MB Step 1 : FROM toolshed/requirements ---> 56c9b11e73ab Step 2 : MAINTAINER Sarah Maman ---> Using cache ---> 0f012c7594c1 Step 3 : RUN sh /root/sarah/galaxy/run.sh & ---> Running in 86b498700000 ---> 520dea36d8d6 Removing intermediate container 86b498700000 Successfully built 520dea36d8d6 lancement de galaxy : [root@vm-docker-test galaxy]# docker run -d -p 8090:90 galaxy-docker-sarah 01824848bb97b0416eac805685312e78b94e1298a8ef65292d81c4c63f8cd137 firefox & Puis ouvrir http://127.0.0.1:8090 *************************************************************************************************************************************************** *************************************************************************************************************************************************** *************************************************************************************************************************************************** A partir du code Galaxy v 17 récupéré. Créer un Dockerfile: [root@vm-docker-test galaxy]# more Dockerfile # Galaxy - Docker # # VERSION Galaxy-central FROM toolshed/requirements MAINTAINER Sarah Maman CMD sh /root/sarah/galaxy/run.sh & Attention, port = 8070 (dans galaxy.ini file) construction du galaxy sous Docker: [root@vm-docker-test galaxy]# docker build -t galaxy-docker-sarah2 . Sending build context to Docker daemon 621.8 MB Step 1 : FROM toolshed/requirements ---> 56c9b11e73ab Step 2 : MAINTAINER Sarah Maman ---> Using cache ---> 0f012c7594c1 Step 3 : CMD sh /root/sarah/galaxy/run.sh & ---> Using cache ---> d35775da8708 Successfully built d35775da8708 [root@vm-docker-test galaxy]# docker run -i -t -p 8070:70 galaxy-docker-sarah2 OU : [root@vm-docker-test galaxy]# docker run -d -p 8070:70 galaxy-docker-sarah2 a37a06bec4e0ad5c9c78767ec4659c67de3318a08bd92c28c0fc3f5bb59fb872 AUTRE TEST: [root@vm-docker-test galaxy]# docker build -t galaxy-docker-sarah3 . Sending build context to Docker daemon 621.8 MB Step 1 : FROM toolshed/requirements ---> 56c9b11e73ab Step 2 : MAINTAINER Sarah Maman ---> Using cache ---> 0f012c7594c1 Step 3 : CMD sh /root/sarah/galaxy/run.sh & ---> Using cache ---> d35775da8708 Successfully built d35775da8708 [root@vm-docker-test galaxy]# docker run -d -p 8070:70 -p 8071:71 -p 8072:72 galaxy-docker-sarah3 4ee337f44f8e42a969c76eab34c51932cffe413522987b65bb6205fc91eb66a1 puis firefox & Puis ouvrir http://127.0.0.1:8070