diff --git a/docker_inventory b/docker_inventory deleted file mode 100644 index d2c9f23a..00000000 --- a/docker_inventory +++ /dev/null @@ -1,5 +0,0 @@ -[docker] -localhost ansible_connection=local -[aws] -# Put you aws IP and key here to make FTP work in the default VPC. -# If you want further group-specific variables, put the host in these groups as well [e.g artimed]. diff --git a/docker_metavisitor_inventory b/docker_metavisitor_inventory deleted file mode 100644 index d6f3d444..00000000 --- a/docker_metavisitor_inventory +++ /dev/null @@ -1,5 +0,0 @@ -[metavisitor] -localhost ansible_connection=local -[aws] -# Put you aws IP and key here to make FTP work in the default VPC. -# If you want further group-specific variables, put the host in these groups as well [e.g artimed]. diff --git a/dockerfiles/galaxy-kickstart-artimed/Dockerfile b/dockerfiles/galaxy-kickstart-artimed/Dockerfile index 3e5933df..8117af51 100644 --- a/dockerfiles/galaxy-kickstart-artimed/Dockerfile +++ b/dockerfiles/galaxy-kickstart-artimed/Dockerfile @@ -20,5 +20,5 @@ CMD printenv >> /etc/default/supervisor && bash -c "source /etc/default/supervis --extra-vars nginx_galaxy_location=$NGINX_GALAXY_LOCATION \ --extra-vars galaxy_admin=$GALAXY_CONFIG_ADMIN_USERS \ --extra-vars ftp_upload_site=$IP_ADDRESS \ - -i docker_inventory && \ + -i inventory_files/docker && \ /usr/bin/python /usr/bin/supervisord -c /etc/supervisor/supervisord.conf --nodaemon" diff --git a/dockerfiles/galaxy-kickstart-metavisitor/Dockerfile b/dockerfiles/galaxy-kickstart-metavisitor/Dockerfile index 52188191..0df810d4 100644 --- a/dockerfiles/galaxy-kickstart-metavisitor/Dockerfile +++ b/dockerfiles/galaxy-kickstart-metavisitor/Dockerfile @@ -5,7 +5,7 @@ MAINTAINER Marius van den Beek COPY . /setup WORKDIR /setup -RUN ansible-playbook -i docker_metavisitor_inventory -c local galaxy.yml && \ +RUN ansible-playbook -i inventory_files/metavisitor -c local galaxy.yml && \ apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* # Expose port 80 (webserver), 21 (FTP server), 8800 (Proxy), 9002 (supvisord web app) @@ -20,5 +20,5 @@ CMD printenv >> /etc/default/supervisor && bash -c "source /etc/default/supervis --extra-vars nginx_galaxy_location=$NGINX_GALAXY_LOCATION \ --extra-vars galaxy_admin=$GALAXY_CONFIG_ADMIN_USERS \ --extra-vars ftp_upload_site=$IP_ADDRESS \ - -i docker_metavisitor_inventory && \ + -i inventory_files/metavisitor && \ /usr/bin/python /usr/bin/supervisord -c /etc/supervisor/supervisord.conf --nodaemon" diff --git a/dockerfiles/galaxy-kickstart-metavisitor/Dockerfile-metavisitor b/dockerfiles/galaxy-kickstart-metavisitor/Dockerfile-metavisitor index 3b152f76..71c57752 100644 --- a/dockerfiles/galaxy-kickstart-metavisitor/Dockerfile-metavisitor +++ b/dockerfiles/galaxy-kickstart-metavisitor/Dockerfile-metavisitor @@ -12,5 +12,5 @@ EXPOSE :9002 VOLUME ["/export", "/var/lib/docker"] CMD ansible-playbook galaxy.yml -c local --tags "persists_galaxy,nginx_config,galaxy_config_files,galaxy_extras_job_conf" --skip-tags=skip_supervisor_start_in_docker \ - --extra-vars nginx_galaxy_location=$NGINX_GALAXY_LOCATION -i docker_inventory && \ + --extra-vars nginx_galaxy_location=$NGINX_GALAXY_LOCATION -i inventory_files/docker && \ /usr/bin/python /usr/bin/supervisord -c /etc/supervisor/supervisord.conf --nodaemon diff --git a/dockerfiles/galaxy-kickstart/Dockerfile b/dockerfiles/galaxy-kickstart/Dockerfile index 40f21a3a..fc6c722a 100644 --- a/dockerfiles/galaxy-kickstart/Dockerfile +++ b/dockerfiles/galaxy-kickstart/Dockerfile @@ -20,12 +20,12 @@ ONBUILD RUN DEBIAN_FRONTEND=noninteractive apt-get update && \ COPY . /setup WORKDIR /setup -RUN ansible-playbook -i docker_inventory -c local galaxy.yml +RUN ansible-playbook -i inventory_files/docker -c local galaxy.yml ENV LC_ALL=en_US.UTF-8 \ LANG=en_US.UTF-8 RUN locale-gen en_US.UTF-8 && dpkg-reconfigure locales -RUN ansible-playbook -i docker_inventory -c local galaxy.yml && \ +RUN ansible-playbook -i inventory_files/docker -c local galaxy.yml && \ apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* # work around for AUFS bug @@ -53,5 +53,5 @@ CMD printenv >> /etc/default/supervisor && bash -c "source /etc/default/supervis --extra-vars galaxy_admin=$GALAXY_CONFIG_ADMIN_USERS \ --extra-vars ftp_upload_site=$IP_ADDRESS \ --extra-vars nat_masquerade=$NAT_MAQUERADE \ - -i docker_inventory && \ + -i inventory_files/docker && \ /usr/bin/python /usr/bin/supervisord -c /etc/supervisor/supervisord.conf --nodaemon" diff --git a/extra-files/galaxy-kickstart/galaxy-kickstart_logo.png b/extra-files/galaxy-kickstart/galaxy-kickstart_logo.png new file mode 100644 index 00000000..d943f5bb Binary files /dev/null and b/extra-files/galaxy-kickstart/galaxy-kickstart_logo.png differ diff --git a/extra-files/galaxy-kickstart/galaxy-kickstart_tool_list.yml b/extra-files/galaxy-kickstart/galaxy-kickstart_tool_list.yml new file mode 100644 index 00000000..92b182b4 --- /dev/null +++ b/extra-files/galaxy-kickstart/galaxy-kickstart_tool_list.yml @@ -0,0 +1,37 @@ +tools: +- name: data_manager_fetch_genome_dbkeys_all_fasta + owner: devteam + revisions: + - 776bb1b478a0 + tool_panel_section_label: 'Data Managers' + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: data_manager_bowtie_index_builder + owner: iuc + revisions: + - 0a0c648498e2 + tool_panel_section_label: 'Data Managers' + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: data_manager_bowtie2_index_builder + owner: devteam + revisions: + - e87aeff2cf88 + tool_panel_section_label: 'Data Managers' + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: data_manager_bwa_index_builder + owner: devteam + revisions: + - cc5ae94acf01 + tool_panel_section_label: 'Data Managers' + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: data_manager_bwa_mem_index_builder + owner: devteam + revisions: + - e519769cdb9c + tool_panel_section_label: 'Data Managers' + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: data_manager_twobit_builder + owner: devteam + revisions: + - 74b09c8e5f6e + tool_panel_section_label: 'Data Managers' + tool_shed_url: https://toolshed.g2.bx.psu.edu/ diff --git a/extra-files/galaxy-kickstart/welcome.html b/extra-files/galaxy-kickstart/welcome.html new file mode 100644 index 00000000..1217ac9d --- /dev/null +++ b/extra-files/galaxy-kickstart/welcome.html @@ -0,0 +1,61 @@ + + + + + Homepage + + + + +
+

+ +

+
+
+
+

This Galaxy server instance has been set up by GalaxyKickStarter

+ GalaxyKickStarter Documentation » + GalaxyKickStarter Repository » + +
+ GalaxyKickStarter is developed by ARTbio and installed this Galaxy changeset + +
+ +

Galaxy is now running!

+ + To customize this page edit static/welcome.html + +
+ + Configuring Galaxy » + Installing Tools » + +
+
+ + + +
+

+ + Galaxy is an open platform for supporting data intensive + research. Galaxy is developed by The Galaxy Team + with the support of many contributors. +

+ + + +
+ + + + diff --git a/group_vars/kickstart b/group_vars/kickstart new file mode 100644 index 00000000..9aac3220 --- /dev/null +++ b/group_vars/kickstart @@ -0,0 +1,5 @@ +galaxy_tools_tool_list_files: + - "extra-files/galaxy-kickstart/galaxy-kickstart_tool_list.yml" +additional_files_list: + - { src: "extra-files/galaxy-kickstart/welcome.html", dest: "{{ galaxy_server_dir }}/static/" } + - { src: "extra-files/galaxy-kickstart/galaxy-kickstart_logo.png", dest: "{{ galaxy_server_dir }}/static/images/" } diff --git a/hosts b/hosts deleted file mode 100644 index 9057164f..00000000 --- a/hosts +++ /dev/null @@ -1,10 +0,0 @@ -[artimed] -localhost ansible_ssh_user="root" ansible_ssh_private_key_file="~/.ssh/id_rsa" -[travis_bioblend] -localhost ansible_connection=local -# Uncomment the 2 lines below to point ansible to a local vagrant machine. -#[all] -#localhost ansible_user="vagrant" ansible_port=2222 ansible_private_key_file=.vagrant/machines/default/virtualbox/private_key -[aws] -# Put you aws IP and key here to make FTP work in the default VPC. -# If you want further group-specific variables, put the host in these groups as well [e.g artimed]. diff --git a/inventory_files/artimed b/inventory_files/artimed new file mode 100644 index 00000000..b9442288 --- /dev/null +++ b/inventory_files/artimed @@ -0,0 +1,5 @@ +[artimed] +localhost ansible_connection=local + +# change to the line below if remote target host +# ansible_ssh_user="root" ansible_ssh_private_key_file="" diff --git a/inventory_files/aws b/inventory_files/aws new file mode 100644 index 00000000..95496d4e --- /dev/null +++ b/inventory_files/aws @@ -0,0 +1,7 @@ +[aws] +# adapt the lines below by putting your aws IP and private key to make FTP work in the default AWS VPC (Virtual Private Cloud). + ansible_ssh_user="" ansible_ssh_private_key_file="" + +# *In addition*, adapt the group-specific variables below (here [kickstart], but you can change it, e.g [metavisitor]) +[kickstart] + ansible_ssh_user="" ansible_ssh_private_key_file="" diff --git a/inventory_files/docker b/inventory_files/docker new file mode 100644 index 00000000..c368d75b --- /dev/null +++ b/inventory_files/docker @@ -0,0 +1,2 @@ +[docker] +localhost ansible_connection=local diff --git a/inventory_files/galaxy-kickstart b/inventory_files/galaxy-kickstart new file mode 100644 index 00000000..f1da7aa0 --- /dev/null +++ b/inventory_files/galaxy-kickstart @@ -0,0 +1,5 @@ +[kickstart] +localhost ansible_connection=local + +# if remote target, replace the above line by +# ansible_ssh_user="root" ansible_ssh_private_key_file="" \ No newline at end of file diff --git a/inventory_files/metavisitor b/inventory_files/metavisitor new file mode 100644 index 00000000..f0a0facc --- /dev/null +++ b/inventory_files/metavisitor @@ -0,0 +1,5 @@ +[metavisitor] +localhost ansible_connection=local + +# change with the line bellow if remote target host +# ansible_ssh_user="root" ansible_ssh_private_key_file="" \ No newline at end of file diff --git a/inventory_files/vagrant b/inventory_files/vagrant new file mode 100644 index 00000000..a6b1d5a1 --- /dev/null +++ b/inventory_files/vagrant @@ -0,0 +1,5 @@ +# use this inventory file to target a VM set up using vagrant +# adapt the group variable (here [kickstart]) as you wish + +[kickstart] +localhost ansible_ssh_user="vagrant" ansible_port=2222 ansible_private_key_file="~/ansible-artimed/.vagrant/machines/default/virtualbox/private_key"