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moved all tasks (except nginx) from galaxyextras repo
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,15 @@ | ||
| - hosts: localhost | ||
| connection: local | ||
| remote_user: root | ||
| vars: | ||
| flower_python_package_version: 1.2.0 | ||
| flower_custom_logging: false | ||
| flower_conf_dir: "{{ flower_conf_path | dirname }}" | ||
| flower_ui_users: [] | ||
| roles: | ||
| - role: galaxy-flower | ||
| tasks: | ||
| - name: Add url prefix to flower config | ||
| lineinfile: | ||
| path: "{{ flower_conf_path }}" | ||
| line: 'url_prefix = "{{ flower_url_prefix }}"' |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,32 @@ | ||
| - hosts: localhost | ||
| connection: local | ||
| remote_user: root | ||
| tasks: | ||
| - name: "Install most of the conditional dependencies" | ||
| # https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/dependencies/conditional-requirements.txt | ||
| pip: | ||
| name: "{{item}}" | ||
| virtualenv: "{{ galaxy_venv_dir }}" | ||
| virtualenv_command: "{{ pip_virtualenv_command | default( 'virtualenv' ) }}" | ||
| extra_args: --index-url https://wheels.galaxyproject.org/simple --extra-index-url https://pypi.python.org/simple | ||
| become: True | ||
| become_user: "{{ galaxy_user_name }}" | ||
| with_items: | ||
| - "psycopg2-binary==2.9.9" | ||
| - "mysqlclient" | ||
| - "fluent-logger" | ||
| - "sentry-sdk[fastapi]" | ||
| - "pbs_python" | ||
| - "drmaa" | ||
| - "statsd" | ||
| - "azure-storage-blob==12.19.1" | ||
| - "python-irodsclient==2.0.0" | ||
| - "python-ldap==3.4.0" | ||
| - "ldap3==2.9.1" | ||
| - "python-pam" | ||
| - "galaxycloudrunner" | ||
| - "pkce" | ||
| - "total-perspective-vortex>=2.3.2,<3" | ||
| - "pykube-ng==21.3.0" | ||
| - "kamaki" | ||
| - "boto3" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,10 @@ | ||
| - hosts: localhost | ||
| connection: local | ||
| remote_user: root | ||
| tasks: | ||
| - name: "Install Galaxy job conf" | ||
| template: src=job_conf.xml.j2 dest={{ galaxy_job_conf_path }} owner={{ galaxy_user_name }} group={{ galaxy_user_name }} | ||
|
|
||
| - name: "Install Galaxy container resolution configuration" | ||
| template: src=container_resolvers_conf.yml.j2 dest={{ galaxy_container_resolvers_conf_path }} owner={{ galaxy_user_name }} group={{ galaxy_user_name }} | ||
| when: galaxy_container_resolution | bool |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| - hosts: localhost | ||
| connection: local | ||
| remote_user: root | ||
| tasks: | ||
| - name: "Setup job metrics" | ||
| template: src=job_metrics_conf.yml.j2 dest={{ galaxy_job_metrics_conf_path }} owner={{ galaxy_user_name }} group={{ galaxy_user_name }} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| - hosts: localhost | ||
| connection: local | ||
| remote_user: root | ||
| tasks: | ||
| - name: "Run common_startup.sh to build the galaxy client" | ||
| shell: scripts/common_startup.sh | ||
| environment: | ||
| GALAXY_VIRTUAL_ENV: "{{ galaxy_venv_dir }}" | ||
| args: | ||
| chdir: "{{ galaxy_server_dir }}" | ||
| become: True | ||
| become_user: "{{ galaxy_user_name }}" | ||
|
|
||
| - name: "Install watchdog for galaxy" | ||
| pip: | ||
| name: "watchdog" | ||
| virtualenv: "{{ galaxy_venv_dir }}" | ||
| virtualenv_command: "{{ pip_virtualenv_command | default( 'virtualenv' ) }}" | ||
| extra_args: --index-url https://wheels.galaxyproject.org/simple --extra-index-url https://pypi.python.org/simple | ||
| become: True | ||
| become_user: "{{ galaxy_user_name }}" | ||
|
|
||
| - name: Ensure galaxy_logs dir exists | ||
| file: path={{ galaxy_logs_dir }} state=directory owner={{ galaxy_user_name }} group={{ galaxy_user_name }} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| - hosts: localhost | ||
| connection: local | ||
| remote_user: root | ||
| tasks: | ||
| - name: "Install galaxy user creation script." | ||
| template: src=create_galaxy_user.py.j2 dest=/usr/local/bin/create_galaxy_user.py mode=a+x | ||
|
|
||
| - name: "Install galaxy check database script." | ||
| template: src=check_database.py.j2 dest=/usr/local/bin/check_database.py mode=a+x | ||
|
|
||
| - name: "Install export user files script." | ||
| template: src=export_user_files.py.j2 dest=/usr/local/bin/export_user_files.py mode=a+x | ||
|
|
||
| - name: "Install add_tool_shed script." | ||
| template: src=add_tool_shed.py.j2 dest=/usr/local/bin/add-tool-shed mode=a+x | ||
|
|
||
| - name: "Install startup lite script." | ||
| template: src=startup_lite.sh.j2 dest=/usr/bin/startup_lite mode=a+x | ||
|
|
||
| - name: "Install cgroupfs_mount.sh for startup script." | ||
| template: src=cgroupfs_mount.sh.j2 dest=/root/cgroupfs_mount.sh mode=a+x | ||
|
|
||
| - name: "Install update_yaml_value script." | ||
| template: src=update_yaml_value.py.j2 dest=/usr/local/bin/update_yaml_value mode=a+x |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,28 @@ | ||
| - hosts: localhost | ||
| connection: local | ||
| remote_user: root | ||
| tasks: | ||
| - name: "Install gravity for galaxy" | ||
| pip: | ||
| name: gravity | ||
| version: 1.0.6 | ||
| virtualenv: "{{ galaxy_venv_dir }}" | ||
| virtualenv_command: "{{ pip_virtualenv_command | default( 'virtualenv' ) }}" | ||
| extra_args: "--index-url https://wheels.galaxyproject.org/ --extra-index-url https://pypi.python.org/simple" | ||
| become: True | ||
| become_user: "{{ galaxy_user_name }}" | ||
|
|
||
| - name: Deploy galaxyctl wrapper script | ||
| copy: | ||
| content: | | ||
| #!/usr/bin/env sh | ||
| export GRAVITY_CONFIG_FILE={{ gravity_config_file }} | ||
| export GRAVITY_STATE_DIR={{ gravity_state_dir }} | ||
| exec sudo -E -u $GALAXY_USER {{ galaxy_venv_dir }}/bin/galaxyctl "$@" | ||
| dest: "/usr/local/bin/galaxyctl" | ||
| mode: "0755" | ||
| become: True | ||
| become_user: root | ||
|
|
||
| - name: "Install Gravity conf" | ||
| template: src=gravity.yml.j2 dest={{ gravity_config_file }} owner={{ galaxy_user_name }} group={{ galaxy_user_name }} |
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