diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index b4daac2..9798bbf 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -23,6 +23,7 @@ jobs: - name: Copy files to test instance and preserve secrets and hosts run: | rsync -rav * debian@usegalaxy-test.cerit-sc.cz:~/usegalaxy-${{ steps.date.outputs.date }} + ssh debian@usegalaxy-test.cerit-sc.cz 'cp ~/usegalaxy/group_vars/secret.yml ~/usegalaxy-${{ steps.date.outputs.date }}/group_vars' ssh debian@usegalaxy-test.cerit-sc.cz 'cp ~/usegalaxy/hosts ~/usegalaxy-${{ steps.date.outputs.date }}' ssh debian@usegalaxy-test.cerit-sc.cz 'cp ~/usegalaxy/.vault-password.txt ~/usegalaxy-${{ steps.date.outputs.date }}' - name: Run playbook diff --git a/README.md b/README.md index b019ec1..1f2da4e 100644 --- a/README.md +++ b/README.md @@ -73,22 +73,49 @@ The api key can be found in the User -> Preferences -> Manage API Key in Galaxy Later we should use this [role](https://github.com/galaxyproject/ansible-galaxy-tools) to automate this, but there are too many tools to be installed and it is very inpractical for testing purposes. -## Notes +## Debian 11 + +### TUS On ubuntu < 22.04 and Debian < 12 the GLIBC version is incompatible with the ```galaxyproject.tusd``` GLIBC, therfore playbook ends in error. - in `roles/galaxyproject.tusd/defaults/main.yml` you have to set the `tusd_version:` to 'v1.8.0' (tested, possibly higher) -# Debian 11 +### Ansible On Debian 11 the default version of `ansible` is 2.10.08 which fails to extract binaries for TUSd. -- workaround: - - `sudo vim /etc/apt/sources.list` add this line : `deb http://ppa.launchpad.net/ansible/ansible/ubuntu focal main` +- workaround: + - because of Puppet, we need to create dedicated sources.list file for ansible + - `sudo vim /etc/apt/sources.list.d/ansible_ubuntu_focal_main.list` add this line : `deb http://ppa.launchpad.net/ansible/ansible/ubuntu focal main` - then `sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 93C4A3FD7BB9C367` - followed by `sudo apt-get update` and `sudo apt-get install ansible -y` - Note that you might need to `sudo apt remove ansible` `sudo apt autoremove` before you try to install ansible. +### Nginx Upload Module + +Our playbook makes use of `nginx-upload-module`, which is not included by default in any nginx-* distribution from `apt`. +This is a simple recipe for installing nginx with the upload-module. + +``` +sudo apt remove *nginx* -y && +sudo apt autoremove -y && + +wget http://nginx.org/download/nginx-1.24.0.tar.gz && +tar -xzf nginx-1.24.0.tar.gz && +cd nginx-1.24.0/ && +git clone https://github.com/hongzhidao/nginx-upload-module.git && +sudo apt-get install -y libpcre3 libpcre3-dev libssl-dev zlib1g-dev && +./configure --user=nginx --group=nginx --prefix=/etc/nginx --conf-path=/etc/nginx/nginx.conf --sbin-path=/usr/sbin/nginx --http-log-path=/var/log/nginx/access.log --error-log-path=/var/log/nginx/error.log --lock-path=/var/lock/nginx.lock --pid-path=/run/nginx.pid --modules-path=/usr/lib/nginx/modules --http-client-body-temp-path=/var/lib/nginx/body --http-fastcgi-temp-path=/var/lib/nginx/fastcgi --http-proxy-temp-path=/var/lib/nginx/proxy --http-scgi-temp-path=/var/lib/nginx/scgi --http-uwsgi-temp-path=/var/lib/nginx/uwsgi --with-compat --with-debug --with-pcre-jit --with-http_ssl_module --with-http_stub_status_module --with-http_realip_module --with-http_auth_request_module --with-http_v2_module --with-http_dav_module --with-http_slice_module --with-threads --with-http_addition_module --with-http_gunzip_module --with-http_gzip_static_module --with-http_sub_module --add-module=nginx-upload-module && +make && make install +``` + +Note that you might need to `sudo systemctl unmask nginx.service` and remove the `galaxy` and `redirect-ssl` from `/etc/nginx/sites-available and `/etc/nginx/sites-enabled` before running the playbook again. + +### Other issues + + Use `sudo apt install python3-docker` before running the `usegalaxy.rabbitmqserver` role. For influxdb apt key error: https://www.influxdata.com/blog/linux-package-signing-key-rotation/ For proftpd add "LoadModule mod_tls.c" to roles/galaxyproject.proftpd/templates/tls.conf.j2 just before the TLSEngine + diff --git a/add_group_users.py b/add_group_users.py new file mode 100755 index 0000000..51b46b2 --- /dev/null +++ b/add_group_users.py @@ -0,0 +1,36 @@ +import psycopg2 +import bioblend.galaxy +import sys + +conn = psycopg2.connect(database="galaxy", user="postgres") +cursor = conn.cursor() +cursor.execute("SELECT * FROM galaxy_user") +users = cursor.fetchall() +user_dict = dict() + +for user in users: + user_dict[user[0]] = user[3] # id is key, email is value + +cursor.execute("SELECT * FROM custos_authnz_token") +einfra_users = cursor.fetchall() + +einfra_emails = [] +for einfra_user in einfra_users: + einfra_emails.append(user_dict[einfra_user[1]]) + +server = 'https://' + sys.argv[1] +api_key = sys.argv[2] +gi = bioblend.galaxy.GalaxyInstance(url=server, key=api_key) + +api_users = gi.users.get_users() +id_dict = dict() +for user in api_users: + id_dict[user['email']] = user['id'] + +groups = gi.groups.get_groups() +for group in groups: + if group['name'] == 'E-infra': + group_id = group['id'] + +for mail in einfra_emails: + gi.groups.add_group_user(group_id=group_id, user_id=id_dict[mail]) diff --git a/ansible.cfg b/ansible.cfg index a552000..7ba20e1 100644 --- a/ansible.cfg +++ b/ansible.cfg @@ -1,12 +1,13 @@ [defaults] +#no_log = True log_path = /var/log/ansible.log interpreter_python = /usr/bin/python3 inventory = hosts stdout_callback = yaml bin_ansible_callbacks = True - retry_files_enabled = false vault_password_file = .vault-password.txt +gather_subset=!hardware # Show diffs of changes [diff] diff --git a/eu_tool_list.yaml b/eu_tool_list.yaml new file mode 100644 index 0000000..16d6328 --- /dev/null +++ b/eu_tool_list.yaml @@ -0,0 +1,15134 @@ +tools: +- name: iedb_api + owner: iuc + revisions: + - 7ed6dda64a81 + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: sra_tools + owner: iuc + revisions: + - 6ea73833cf67 + - f5ea3ce9b9b0 + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ncbi_acc_download + owner: iuc + revisions: + - e063168e0a81 + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: uniprotxml_downloader + owner: galaxyp + revisions: + - a371252a2cf6 + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: unipept + owner: galaxyp + revisions: + - 7863f1abcdda + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ncbi_eutils_esearch + owner: iuc + revisions: + - 30150bd36c9a + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ncbi_eutils_egquery + owner: iuc + revisions: + - 28f69754ddc5 + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ncbi_eutils_ecitmatch + owner: iuc + revisions: + - 732a52c18758 + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ncbi_eutils_epost + owner: iuc + revisions: + - 196b8dd07896 + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ncbi_eutils_elink + owner: iuc + revisions: + - 2791c731fc65 + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ncbi_eutils_einfo + owner: iuc + revisions: + - 5b1dc5936af2 + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ncbi_eutils_esummary + owner: iuc + revisions: + - c8d4ea6376a7 + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ncbi_eutils_efetch + owner: iuc + revisions: + - 0fc65a60436f + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: uniprot_rest_interface + owner: bgruening + revisions: + - 054483e27a35 + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ensembl_get_sequences + owner: earlhaminst + revisions: + - 7af66c2b3831 + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ensembl_get_genetree + owner: earlhaminst + revisions: + - 515e7181d5e9 + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ensembl_get_feature_info + owner: earlhaminst + revisions: + - d6bb417dc831 + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: enasearch_search_data + owner: iuc + revisions: + - 6e692d5a5599 + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: enasearch_retrieve_data + owner: iuc + revisions: + - 0719cfc3ebcb + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: enasearch_retrieve_taxons + owner: iuc + revisions: + - 8881ac3eebd7 + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: enasearch_retrieve_analysis_report + owner: iuc + revisions: + - a5f787bfe69e + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: enasearch_retrieve_run_report + owner: iuc + revisions: + - ccc0e55c9e16 + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ebi_search_rest_results + owner: iuc + revisions: + - 42d5e40fcd0b + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ebi_metagenomics_run_downloader + owner: iuc + revisions: + - a1ef6c88ee37 + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ega_download_client + owner: iuc + revisions: + - f9db47f68e5e + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: dbbuilder + owner: galaxyp + revisions: + - 983bf725dfc2 + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ncbi_datasets + owner: iuc + revisions: + - 1e188c9610c3 + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: pysradb_search + owner: iuc + revisions: + - b91e1e70f3a1 + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: spocc_occ + owner: ecology + revisions: + - f64b3c1a80a6 + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ena_upload + owner: iuc + revisions: + - a62c4a11a67d + tool_panel_section_label: Send Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: curl_post + owner: imgteam + revisions: + - 7f9434fc9d4c + tool_panel_section_label: Send Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: split_file_on_column + owner: bgruening + revisions: + - 37a53100b67e + tool_panel_section_label: Collection Operations + tool_shed_url: toolshed.g2.bx.psu.edu +- name: split_file_to_collection + owner: bgruening + revisions: + - 6cbe2f30c2d7 + tool_panel_section_label: Collection Operations + tool_shed_url: toolshed.g2.bx.psu.edu +- name: collapse_collections + owner: nml + revisions: + - 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5d9a36073ed6 + tool_panel_section_label: QIIME 2 + tool_shed_url: toolshed.g2.bx.psu.edu +- name: qiime2__deblur__denoise_16s + owner: q2d2 + revisions: + - 2572fc0f88f2 + tool_panel_section_label: QIIME 2 + tool_shed_url: toolshed.g2.bx.psu.edu +- name: t2t_report + owner: devteam + revisions: + - 592acb9505fc + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: toolshed.g2.bx.psu.edu +- name: t2ps + owner: devteam + revisions: + - 4d9910e996f7 + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: toolshed.g2.bx.psu.edu +- name: poisson2test + owner: devteam + revisions: + - 5ff18ec88181 + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: toolshed.g2.bx.psu.edu +- name: lca_wrapper + owner: devteam + revisions: + - 33e8ed5a4601 + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: toolshed.g2.bx.psu.edu +- name: gi2taxonomy + owner: devteam + revisions: + - 7b1b03c4465d + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: toolshed.g2.bx.psu.edu +- name: find_diag_hits + owner: devteam + revisions: + - acf51ff24c7d + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: toolshed.g2.bx.psu.edu +- name: count_covariates + owner: devteam + revisions: + - 14e304b70425 + tool_panel_section_label: GATK Tools + tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/files/galaxy/config/tpv_rules_local.yml b/files/galaxy/config/tpv_rules_local.yml index dfda45c..0573742 100644 --- a/files/galaxy/config/tpv_rules_local.yml +++ b/files/galaxy/config/tpv_rules_local.yml @@ -327,14 +327,10 @@ tools: # params: # walltime: "{int(job.get_param_values(app)['__job_resource']['time'])}" -# .*/bwa/.*: -# scheduling: -# require: -# - pulsar -# .*/bwa_mem/.*: -# scheduling: -# require: -# - pulsar + .*/alphafold/.*: + scheduling: + require: + - pulsar_gpu #roles: # training.*: @@ -353,7 +349,7 @@ destinations: params: tmp_dir: true scheduling: - rejecVCt: + reject: - pulsar - singularity tpv_local_singularity: diff --git a/files/galaxy/tools/testing.xml b/files/galaxy/tools/testing.xml index 6db2e85..3a5e766 100644 --- a/files/galaxy/tools/testing.xml +++ b/files/galaxy/tools/testing.xml @@ -1,12 +1,15 @@ - + - "$output1"]]> + - + + - + + diff --git a/files/galaxy/welcome.html b/files/galaxy/welcome.html index 5cb8978..549c600 100644 --- a/files/galaxy/welcome.html +++ b/files/galaxy/welcome.html @@ -1,19 +1,31 @@ - - - + + + -
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Dear users, we are still in testing mode, so we kindly ask you to report any troubles at regalaxy@rt.cesnet.cz. So far, we know that a few tools are incompatible with the latest Galaxy version. Sometimes your jobs may end up in the Error state or even in the Complete state (but empty with 0 size) with messages like: =>> PBS: job killed:... That means the resources need to be fit to means of the tool, and reporting this fact will help us improve the service. On behalf of the admin group, thank you. -

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Welcome to UseGalaxy CZ

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diff --git a/galaxy.yml b/galaxy.yml index 119e085..868af98 100644 --- a/galaxy.yml +++ b/galaxy.yml @@ -17,14 +17,14 @@ path: "{{ postgresql_backup_dir }}/pg_dump" state: directory owner: postgres - group: "{{ galaxy_user_name }}" + group: "{{ galaxy_user_group }}" mode: 0750 - name: Create initial empty pg_dump file if needed # otherwise the following logrotate conf will not work file: path: "{{ postgresql_backup_dir }}/pg_dump/{{ postgresql_pg_dump_prefix }}.sql.gz" state: touch owner: postgres - group: "{{ galaxy_user_name }}" + group: "{{ galaxy_user_group }}" mode: 0640 - name: Set-up Galaxy DB backup using pg_dump and logrotate ansible.builtin.blockinfile: @@ -52,7 +52,11 @@ vars_files: - group_vars/secret.yml pre_tasks: - - pip: + - name: Install Dependencies + ansible.builtin.package: + name: ['acl', 'bzip2', 'git', 'make', 'tar', 'python3-bioblend', 'python3-venv', 'python3-setuptools', 'python3-pip', 'python3-psycopg2', 'rsync', 'python3-docker', 'nginx-full'] + - name: Install additional pip packages + ansible.builtin.pip: name: passlib - htpasswd: path: /etc/nginx/passwd @@ -61,9 +65,6 @@ owner: www-data # nginx on centos group: root mode: 0640 - - name: Install Dependencies - package: - name: ['acl', 'bzip2', 'git', 'make', 'tar', 'python3-bioblend', 'python3-venv', 'python3-setuptools', 'python3-pip', 'python3-psycopg2', 'rsync', 'nginx-full'] - name: Install RHEL/CentOS/Rocky specific dependencies package: name: ['tmpwatch'] @@ -73,17 +74,56 @@ name: ['tmpreaper'] when: ansible_os_family == 'Debian' - name: Ensure the python command exists - ansible.builtin.shell: which python + ansible.builtin.shell: + cmd: which python||exit 0 register: python_path - name: Register python3 path - ansible.builtin.shell: which python3 + ansible.builtin.command: which python3 register: python3_path + when: python_path.stdout == "" - name: Link python to python3 if missing ansible.builtin.file: src: python3_path.stdout dest: python3_path.stdout[:-1] state: link + force: yes when: python_path.stdout == "" + - git: + repo: 'https://github.com/usegalaxy-eu/libraries-training-repo' + dest: /libraries/ + when: "'usegalaxy' in inventory_hostname" +# - name: Create data storage for UMSA +# file: +# owner: "{{ galaxy_user_name }}" +# group: "{{ galaxy_user_group }}" +# path: "{{ galaxy_data_prefix }}" +# state: directory +# mode: "0755" +# when: "'umsa' in inventory_hostname" + - name: Create the RBD storage directory + file: + owner: "{{ galaxy_user_name }}" + group: "{{ galaxy_user_group }}" + path: /rbd/data + state: directory + mode: '0755' + when: "'usegalaxy' in inventory_hostname" + - name: Create the nginx upload job files store + file: + owner: www-data + group: "{{ galaxy_user_group }}" + path: /rbd/data/_upload_job_files + state: directory + mode: '0775' + when: "'usegalaxy' in inventory_hostname" + - name: Create the client body temp path + file: + owner: www-data + group: "{{ galaxy_user_group }}" + path: /rbd/data/nginx_upload_store + state: directory + mode: '0775' + when: "'usegalaxy' in inventory_hostname" ## pre tasks specific for galaxy-re - name: Setup NBD client ansible.builtin.lineinfile: @@ -113,23 +153,6 @@ opts: rw,_netdev state: mounted when: "'galaxy-re' in inventory_hostname or 'galaxy-re' in ansible_hostname" - - post_tasks: - - name: Setup gxadmin cleanup task - ansible.builtin.cron: - name: "Cleanup Old User Data" - user: "{{ galaxy_user_name }}" # Run as the Galaxy user - minute: "0" - hour: "0" - job: "GALAXY_LOG_DIR=/tmp/gxadmin/ GALAXY_ROOT={{ galaxy_root }}/server /usr/local/bin/gxadmin galaxy cleanup 60" - - name: RE Galaxy instance patch in lib/galaxy/webapps/galaxy/api/job_files.py - replace: - path: "{{ galaxy_root }}/server/lib/galaxy/webapps/galaxy/api/job_files.py" -# after: '^\s*?try:' - regexp: '^(\s*?)shutil\.move\(input_file\.name,\s*path\)\s*$' - replace: '\1os.chmod(shutil.move(input_file.name, path), 0o664)' - validate: 'python -m py_compile %s' - when: "'galaxy-re' in inventory_hostname or 'galaxy-re' in ansible_hostname" roles: - galaxyproject.tusd - galaxyproject.galaxy @@ -143,4 +166,30 @@ - galaxyproject.proftpd - geerlingguy.docker - usegalaxy_eu.rabbitmqserver +# - galaxyproject.tiaas2 - galaxyproject.gxadmin +# - galaxyproject.cvmfs +# - dj-wasabi.telegraf + post_tasks: + - name: Setup gxadmin cleanup task + ansible.builtin.cron: + name: "Cleanup Old User Data" + user: "{{ galaxy_user_name }}" # Run as the Galaxy user + minute: "0" + hour: "0" + job: "GALAXY_LOG_DIR=/tmp/gxadmin/ GALAXY_ROOT={{ galaxy_root }}/server /usr/local/bin/gxadmin galaxy cleanup 60" + - name: Setup user - group association rutine + ansible.builtin.cron: + name: "Add E-infra users to E-infra group" + user: postgres # Run as the postgres user + minute: "0" + hour: "*" + job: "python3 {{ playbook_dir }}/add_group_users.py {{ inventory_hostname }} {{ api_key }}" + when: "'usegalaxy' in inventory_hostname" + - name: RE Galaxy instance patch in lib/galaxy/webapps/galaxy/api/job_files.py + replace: + path: "{{ galaxy_root }}/server/lib/galaxy/webapps/galaxy/api/job_files.py" + regexp: '^(\s*?)shutil\.move\(input_file\.name,\s*path\)\s*$' + replace: '\1os.chmod(shutil.move(input_file.name, path), 0o664)' + validate: 'python -m py_compile %s' + when: "'galaxy-re' in inventory_hostname or 'galaxy-re' in ansible_hostname" diff --git a/group_vars/all.yml b/group_vars/all.yml index fe0056a..21027a1 100644 --- a/group_vars/all.yml +++ b/group_vars/all.yml @@ -4,5 +4,38 @@ pip_virtualenv_command: /usr/bin/python3 -m venv # usegalaxy_eu.certbot, usegal # Common variables needed by all hosts galaxy_user_name: galaxyelixir +galaxy_user_id: 10145 +galaxy_user_group: galaxyelixir galaxy_db_name: galaxyelixir galaxy_data_dir: "/mnt/galaxy-re" +#galaxy_data_prefix: "/mnt/data" + +# CVMFS vars +cvmfs_role: client +galaxy_cvmfs_repos_enabled: config-repo +cvmfs_quota_limit: 500 + +# Telegraf +telegraf_agent_package_state: latest + +# Configure the output to point to an InfluxDB +# running on localhost, and # place data in the +# database "telegraf" which will be created if need be. +telegraf_agent_output: + - type: influxdb + config: + - urls = ["http://127.0.0.1:8086"] + - database = "telegraf" + +# The default plugins, applied to any telegraf-configured host +telegraf_plugins_default: + - plugin: cpu + - plugin: disk + - plugin: kernel + - plugin: processes + - plugin: io + - plugin: mem + - plugin: system + - plugin: swap + - plugin: net + - plugin: netstat diff --git a/group_vars/dbservers.yml b/group_vars/dbservers.yml index d1268f8..a572ecd 100644 --- a/group_vars/dbservers.yml +++ b/group_vars/dbservers.yml @@ -6,6 +6,33 @@ postgresql_objects_databases: - name: "{{ galaxy_db_name }}" owner: "{{ galaxy_user_name }}" +postgresql_objects_privileges: + - database: galaxy + roles: telegraf + privs: SELECT + objs: ALL_IN_SCHEMA + +# - database: galaxy +# roles: tiaas +# objs: galaxy_user,galaxy_session,job,history,workflow,workflow_invocation +# type: table +# privs: SELECT +# - database: galaxy +# roles: tiaas +# objs: user_group_association,galaxy_group,role,group_role_association +# type: table +# privs: SELECT,INSERT +# - database: galaxy +# roles: tiaas +# objs: group_role_association +# type: table +# privs: DELETE +# - database: galaxy +# roles: tiaas +# objs: role_id_seq,galaxy_group_id_seq,group_role_association_id_seq,user_group_association_id_seq +# type: sequence +# privs: USAGE,SELECT + # PostgreSQL Backups postgresql_backup_dir: "{{ galaxy_data_dir }}/backups" postgresql_backup_local_dir: "{{ galaxy_data_dir }}/backups/scripts" diff --git a/group_vars/galaxyservers.yml b/group_vars/galaxyservers.yml index d7529b6..225f8c4 100644 --- a/group_vars/galaxyservers.yml +++ b/group_vars/galaxyservers.yml @@ -6,20 +6,21 @@ galaxy_manage_paths: true # False by default as your administrator might e.g. ha galaxy_manage_cleanup: true galaxy_layout: root-dir galaxy_root: /srv/galaxy -#galaxy_data_dir: /data -#galaxy_data_dir: /mnt/galaxy-re # defined in all.yml galaxy_tool_dependency_dir: "{{ galaxy_mutable_data_dir }}/dependencies" -galaxy_user: {name: "{{ galaxy_user_name }}", shell: /bin/bash} +galaxy_user: + name: "{{ galaxy_user_name }}" + uid: "{{ galaxy_user_id }}" + group: "{{ galaxy_user_group }}" + shell: /bin/bash # 1ad49865fbeb03551cf7774dc0c12e5cd27ff797 commit_id z galaxy-cz # 7a9ba0c6529d72517c7627422eac16eadff15b46 commit_id posledne, ktore fungovalo #galaxy_commit_id: release_23.0 # 7a9ba0c6529d72517c7627422eac16eadff15b46 # release_23.0 galaxy_commit_id: 72070dbd0a6d0f418d0b8f914825ea2b8e6a0a88 #galaxy_force_checkout: true - miniconda_prefix: "{{ galaxy_tool_dependency_dir }}/conda" -miniconda_version: 4.12.0 -miniconda_base_env_packages: ['mamba'] +miniconda_version: 'latest' # 23.5.2 # 23.5.0 # 4.12.0 miniconda_channels: ['conda-forge', 'bioconda', 'iuc', 'r', 'anaconda', 'petrnovak', 'defaults'] +miniconda_base_env_packages: ['mamba'] singularity_local_cache_dir: "{{ galaxy_mutable_data_dir }}/cache/singularity" @@ -63,7 +64,6 @@ galaxy_job_config: assign: ['db-skip-locked'] execution: default: tpv_dispatcher -# default: pulsar environments: local: runner: local_runner @@ -189,11 +189,6 @@ galaxy_job_config: tpv_config_files: # - https://raw.githubusercontent.com/galaxyproject/tpv-shared-database/main/tools.yml - "{{ tpv_config_dir }}/tpv_rules_local.yml" -# resources: -# default: default -# groups: -# default: [] -# testing: [cores, time] tools: - class: local # these special tools that aren't parameterized for remote execution - expression tools, upload, etc environment: local @@ -286,7 +281,7 @@ galaxy_config: gravity: process_manager: systemd galaxy_root: "{{ galaxy_root }}/server" - galaxy_user: "{{ galaxy_user_name }}" + galaxy_user: "{{ galaxy_user.name }}" virtualenv: "{{ galaxy_venv_dir }}" umask: 022 gunicorn: @@ -437,6 +432,7 @@ pip_install_packages: - python-ldap # RabbitMQ +rabbitmq_hostname: "{{ inventory_hostname }}" rabbitmq_container: name: rabbit_hole image: rabbitmq:3.11-management @@ -504,8 +500,8 @@ flower_broker_api: "https://flower:{{ rabbitmq_users_password.flower }}@localhos flower_broker_url: "pyamqp://flower:{{ rabbitmq_users_password.flower }}@localhost:5671/galaxy_internal?ssl=1" #flower_broker_url: "pyamqp://flower:{{ rabbitmq_users_password.flower }}@{{ inventory_hostname }}:5671/galaxy_internal?ssl=1" flower_proxy_prefix: /flower -flower_user: "{{ galaxy_user_name }}" -flower_group: "{{ galaxy_user_name }}" +flower_user: "{{ galaxy_user.name }}" +flower_group: "{{ galaxy_user.group }}" flower_ui_users: - name: admin password: "{{ flower_admin_password }}" @@ -513,27 +509,6 @@ flower_ui_users: flower_environment_variables: GALAXY_CONFIG_FILE: "{{ galaxy_config_file }}" -# Telegraf -telegraf_plugins_extra: - listen_galaxy_routes: - plugin: "statsd" - config: - - service_address = ":8125" - - metric_separator = "." - - allowed_pending_messages = 10000 - monitor_galaxy_queue: - plugin: "exec" - config: - - commands = ["/usr/bin/env PGDATABASE=galaxy /usr/local/bin/gxadmin iquery queue-overview --short-tool-id"] - - timeout = "10s" - - data_format = "influx" - - interval = "15s" - -# TIaaS setup -tiaas_dir: /srv/tiaas -tiaas_admin_user: admin -tiaas_admin_pass: changeme - # Proftpd: proftpd_galaxy_auth: yes galaxy_ftp_upload_dir: "{{ galaxy_config.galaxy.ftp_upload_dir }}" @@ -543,12 +518,12 @@ proftpd_display_connect: | Unauthorized access is prohibited proftpd_create_ftp_upload_dir: yes proftpd_options: - - User: "{{ galaxy_user_name }}" - - Group: "{{ galaxy_user_name }}" + - User: "{{ galaxy_user.name }}" + - Group: "{{ galaxy_user.group }}" - Port: 21 #proftpd_sql_db: "{{ galaxy_db_name }}?host=/var/run/postgresql" #galaxy@/var/run/postgresql proftpd_sql_db: "{{ galaxy_db_name }}@/var/run/postgresql" -proftpd_sql_user: "{{ galaxy_user_name }}" +proftpd_sql_user: "{{ galaxy_user.name }}" #proftpd_conf_ssl_certificate: /etc/letsencrypt/live/{{ inventory_hostname }}/cert.pem #proftpd_conf_ssl_certificate_key: /etc/letsencrypt/live/{{ inventory_hostname }}/privkey.pem proftpd_conf_ssl_certificate: /etc/ssl/certs/cert.pem @@ -557,4 +532,3 @@ proftpd_global_options: - PassivePorts: 56000 60000 proftpd_use_mod_tls_shmcache: false proftpd_tls_options: NoSessionReuseRequired - diff --git a/hosts b/hosts index f274ea7..d5996a5 100644 --- a/hosts +++ b/hosts @@ -1,4 +1,13 @@ [galaxyservers] galaxy-re.grid.cesnet.cz ansible_connection=local ansible_user=debian +#usegalaxy.cz ansible_connection=local ansible_user=debian +#galaxy-re.grid.cesnet.cz ansible_connection=local ansible_user=debian +#galaxy-umsa.grid.cesnet.cz ansible_connection=local ansible_user=debian [dbservers:children] galaxyservers +[dbservers:children] +galaxyservers +[monitoring] +galaxy-re.grid.cesnet.cz ansible_connection=local ansible_user=debian +[sentryservers] +galaxy-re.grid.cesnet.cz ansible_connection=local ansible_user=debian diff --git a/roles/galaxyproject.nginx/tasks/apt.yml b/roles/galaxyproject.nginx/tasks/apt.yml index d86e036..b1e7118 100644 --- a/roles/galaxyproject.nginx/tasks/apt.yml +++ b/roles/galaxyproject.nginx/tasks/apt.yml @@ -1,10 +1,10 @@ --- -- name: Install nginx (APT) - apt: - pkg: nginx-{{ nginx_flavor }} - notify: - - restart nginx +# - name: Install nginx (APT) +# apt: +# pkg: nginx-{{ nginx_flavor }} +# notify: +# - restart nginx - name: Disable default vhost file: diff --git a/roles/galaxyproject.nginx/tasks/ssl-common.yml b/roles/galaxyproject.nginx/tasks/ssl-common.yml index 3e83bb5..1128aca 100644 --- a/roles/galaxyproject.nginx/tasks/ssl-common.yml +++ b/roles/galaxyproject.nginx/tasks/ssl-common.yml @@ -13,6 +13,17 @@ - reload nginx - supervisorctl restart nginx +#- name: Disable ssl_protocols in nginx.conf if set +# lineinfile: +# name: "{{ nginx_conf_file }}" +# regexp: '^(\s*ssl_protocols\s.*)' +# backrefs: yes +# line: '#\1 # commented by Ansible' +# backup: yes +# notify: +# - reload nginx +# - supervisorctl restart nginx + - name: Configure server-wide SSL template: src: ssl.conf.j2 diff --git a/roles/galaxyproject.tusd/defaults/main.yml b/roles/galaxyproject.tusd/defaults/main.yml index 3fa7cf5..f9f4107 100644 --- a/roles/galaxyproject.tusd/defaults/main.yml +++ b/roles/galaxyproject.tusd/defaults/main.yml @@ -2,7 +2,7 @@ # Use 'latest' to install the latest (stable) release from https://github.com/tus/tusd/releases/, or a valid tag for a # specific tagged release (e.g. v1.7.3) -tusd_version: v1.8.0 # latest +tusd_version: v1.8.0 # Path of the tusd binary tusd_path: /usr/local/sbin/tusd diff --git a/templates/galaxy/config/oidc_backends_config.xml b/templates/galaxy/config/oidc_backends_config.xml index 6ec05c7..23bebdb 100644 --- a/templates/galaxy/config/oidc_backends_config.xml +++ b/templates/galaxy/config/oidc_backends_config.xml @@ -1,10 +1,10 @@ - - 0740f7cc-4573-4a5f-9810-6fd9e57cf6be - 42effa24-73ba-4c05-b3f9-6e75bb3438c171c54b5d-eb9b-441a-8fdf-ab14d5caac9e - https://usegalaxy-test.cerit-sc.cz/authnz/keycloak/callback + + {{ elixir_client_id }} + {{ elixir_client_secret }} + https://{{ inventory_hostname }}/authnz/elixir/callback https://login.e-infra.cz/oidc - https://www.e-infra.cz/img/logo.svg + https://lifescience-ri.eu/fileadmin/lifescience-ri/media/Images/login-grey-wide.jpg.png diff --git a/templates/nginx/galaxy.j2 b/templates/nginx/galaxy.j2 index 7ceb213..05e351d 100644 --- a/templates/nginx/galaxy.j2 +++ b/templates/nginx/galaxy.j2 @@ -37,13 +37,15 @@ server { # Our log files will go to journalctl access_log syslog:server=unix:/dev/log; error_log syslog:server=unix:/dev/log; + # client_body_temp_path {{ galaxy_data_prefix }}/nginx_upload_store; + client_body_buffer_size 1024m; + client_max_body_size 20G; # The most important location block, by default all requests are sent to gunicorn # If you serve galaxy at a path like /galaxy, change that below (and all other locations!) location / { # This is the backend to send the requests to. proxy_pass http://galaxy; - proxy_set_header Host $http_host; proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; proxy_set_header X-Forwarded-Proto $scheme; @@ -55,22 +57,6 @@ server { #auth_ldap_servers ad_1; } - location /api/upload/resumable_upload { - # Disable request and response buffering - proxy_request_buffering off; - proxy_buffering off; - proxy_http_version 1.1; - - # Add X-Forwarded-* headers - proxy_set_header X-Forwarded-Host $host; - proxy_set_header X-Forwarded-Proto $scheme; - - proxy_set_header Upgrade $http_upgrade; - proxy_set_header Connection "upgrade"; - client_max_body_size 0; - proxy_pass http://localhost:{{ galaxy_tusd_port }}/files; - } - # Static files can be more efficiently served by Nginx. Why send the # request to Gunicorn which should be spending its time doing more useful # things like serving Galaxy!