role cleanup

README.md

@@ -25,7 +25,7 @@ pulsar:
   nfs_home: "brno11-elixir"
   nfs_prefix: pulsar-qa2
 
-install_nfs_conda: false
+csnt_install_nfs_conda: false
 
 rabbitmq_hostname: "galaxy-qa2.galaxy.cloud.e-infra.cz"
 rabbitmq_vhost: "pulsar"

group_vars/pulsarservers.yml

@@ -1,32 +1,29 @@
-drmaa_version: 1.0.19
-pbs_server: pbs-m1.metacentrum.cz
-install_nfs_conda: false
-conda_auto_init: "{{ install_nfs_conda }}"
-pulsar_network_homedir: "/storage/{{ pulsar.nfs_home }}/home/{{ pulsar.user_name }}"
+csnt_drmaa_version: 1.0.19
+csnt_pbs_server: pbs-m1.metacentrum.cz
+csnt_install_nfs_conda: false
+csnt_pulsar_network_homedir: "/storage/{{ pulsar.nfs_home }}/home/{{ pulsar.user_name }}"
+csnt_dependency_resolvers: {}
+csnt_pulsar_data_dir: "{{ csnt_pulsar_network_homedir }}/{{ pulsar.nfs_prefix }}"
+csnt_pulsar_cleanup_dir: "{{ csnt_pulsar_data_dir }}/files/cleanup_jobs"
+csnt_pulsar_cleanup_delay: "7d" # DEMON: pulsar-re needs this to have over 30d
+csnt_pulsar_package_change_dir: "{{ pulsar_root }}/venv/lib/python3.11/site-packages/pulsar/client"
 
 # Miniconda settings
-miniconda_prefix: "{{ pulsar_network_homedir }}/conda"
+miniconda_prefix: "{{ csnt_pulsar_network_homedir }}/conda"
 miniconda_exec: "{{ miniconda_prefix }}/bin/mamba"
 miniconda_version: 23.1.0
 miniconda_channels:
   - 'bioconda'
   - 'conda-forge'
-csnt_dependency_resolvers: {}
 
 # only galaxyproject.pulsar role vars below
 pulsar_user: "{{ pulsar.user_name }}"
 pulsar_root: /opt/pulsar
 pulsar_package_version: "0.15.6"
-pulsar_data_dir: "{{ pulsar_network_homedir }}/{{ pulsar.nfs_prefix }}"
-pulsar_staging_dir: "{{ pulsar_data_dir }}/files/staging"
-pulsar_cleanup_dir: "{{ pulsar_data_dir }}/files/cleanup_jobs"
-pulsar_cleanup_delay: "7d" # DEMON: pulsar-re needs this to have over 30d
+pulsar_staging_dir: "{{ csnt_pulsar_data_dir }}/files/staging"
 pulsar_persistence_dir: "{{ pulsar_root }}/files/persistent"
-pulsar_dependencies_dir: "{{ pulsar_data_dir }}/deps"
-pulsar_singularity_cachedir: "{{ pulsar_network_homedir }}/.singularity"
-pulsar_package_change_dir: "{{ pulsar_root }}/venv/lib/python3.11/site-packages/pulsar/client"
+pulsar_dependencies_dir: "{{ csnt_pulsar_data_dir }}/deps"
 pulsar_separate_privileges: true
-pulsar_pip_install: true
 pulsar_pycurl_ssl_library: openssl
 pulsar_systemd: true
 pulsar_systemd_enabled: true
@@ -52,6 +49,7 @@ pulsar_optional_dependencies:
   - psutil
   - pylockfile
 pulsar_yaml_config:
+  conda_auto_init: "{{ csnt_install_nfs_conda }}"
   staging_directory: "{{ pulsar_staging_dir }}"
   persistence_directory: "{{ pulsar_persistence_dir }}"
   tool_dependency_dir: "{{ pulsar_dependencies_dir }}"

host_vars/pulsar-re2.grid.cesnet.cz/vars.yml

@@ -7,14 +7,14 @@ pulsar:
   nfs_home: "brno11-elixir"
   nfs_prefix: pulsar-re
 
-miniconda_channels: 
+miniconda_channels:
   - 'bioconda'
   - 'conda-forge'
   - 'petrnovak'
 miniconda_prefix: "/storage/{{ pulsar.nfs_home }}/home/{{ pulsar.user_name }}/anaconda3"
 miniconda_exec: "{{ miniconda_prefix }}/bin/mamba"
 
-pulsar_cleanup_delay: "40d" # DEMON: pulsar-re* need this to have over 30d
+csnt_pulsar_cleanup_delay: "40d" # DEMON: pulsar-re* need this to have over 30d
 csnt_dependency_resolvers:
   - type: conda
     auto_init: true

pulsar.yml

@@ -37,7 +37,7 @@
     - name: Apply recursive rsync changes in pulsar package
       ansible.posix.patch:
         src: "files/pulsar_repo/{{ pulsar_package_version }}/recursive_rsync.patch"
-        basedir: "{{ pulsar_package_change_dir }}"
+        basedir: "{{ csnt_pulsar_package_change_dir }}"
         backup: true
         strip: 1
     - name: Restart pulsar service after change
@@ -48,13 +48,13 @@
 
     - name: Create .drmaa folder in NFS home
       ansible.builtin.file:
-        path: "{{ pulsar_network_homedir }}/.drmaa"
+        path: "{{ csnt_pulsar_network_homedir }}/.drmaa"
         state: directory
       become: yes
       become_user: "{{ pulsar.user_name }}"
     - name: Create cleanup_jobs dir
       ansible.builtin.file:
-        path: "{{ pulsar_cleanup_dir }}"
+        path: "{{ csnt_pulsar_cleanup_dir }}"
         state: directory
         recurse: yes
         mode: 'a+x'
@@ -65,6 +65,6 @@
         name: "tmpreaper in staging dir"
         minute: "7"
         hour: "*/6"
-        job: "/usr/sbin/tmpreaper --verbose=0 --showdeleted --all --mtime --mtime-dir --runtime=600 {{ pulsar_cleanup_delay }} {{ pulsar_staging_dir }} >> {{ pulsar_cleanup_dir }}/cleaning_pulsar_files.log"
+        job: "/usr/sbin/tmpreaper --verbose=0 --showdeleted --all --mtime --mtime-dir --runtime=600 {{ csnt_pulsar_cleanup_delay }} {{ pulsar_staging_dir }} >> {{ csnt_pulsar_cleanup_dir }}/cleaning_pulsar_files.log"
       become: yes
       become_user: "{{ pulsar.user_name }}"

roles/metacentrum.krbnfs/tasks/main.yml

@@ -6,7 +6,7 @@
       - krb5-user
       - anacron
       - logrotate
-      
+
 - name: Metacentrum repo key
   apt_key:
     url: https://repo.metacentrum.cz/key.asc
@@ -29,12 +29,12 @@
       - nfs-common
 
 - name: PBS config
-  lineinfile: 
+  lineinfile:
     path: /etc/pbs.conf
     regexp: "^{{ item.key }}="
     line: "{{ item.key }}={{ item.value }}"
   loop:
-    - { key: 'PBS_SERVER', value: '{{ pbs_server }}' }
+    - { key: 'PBS_SERVER', value: '{{ csnt_pbs_server }}' }
     - { key: 'PBS_AUTH_METHOD', value: 'GSS' }
     - { key: 'PBS_ENCRYPT_METHOD', value: 'GSS' }
     - { key: 'PBS_SUPPORTED_AUTH_METHODS', value: 'GSS,resvport' }

roles/metacentrum.pulsar/tasks/main.yml

@@ -23,15 +23,15 @@
 
 - name: Download DRMAA
   get_url:
-    url: https://master.dl.sourceforge.net/project/pbspro-drmaa/pbs-drmaa/1.0/pbs-drmaa-{{ drmaa_version }}.tar.gz?viasf=1
-    dest: /tmp/pbs-drmaa-{{ drmaa_version }}.tar.gz
+    url: https://master.dl.sourceforge.net/project/pbspro-drmaa/pbs-drmaa/1.0/pbs-drmaa-{{ csnt_drmaa_version }}.tar.gz?viasf=1
+    dest: /tmp/pbs-drmaa-{{ csnt_drmaa_version }}.tar.gz
 
 - name: Install DRMAA
   shell: |
     cd /tmp
-    rm -rf pbs-drmaa-{{ drmaa_version }}
-    tar xzf pbs-drmaa-{{ drmaa_version }}.tar.gz
-    cd pbs-drmaa-{{ drmaa_version }}
+    rm -rf pbs-drmaa-{{ csnt_drmaa_version }}
+    tar xzf pbs-drmaa-{{ csnt_drmaa_version }}.tar.gz
+    cd pbs-drmaa-{{ csnt_drmaa_version }}
     ./configure --prefix /opt/drmaa
     make && make install
 
@@ -72,13 +72,13 @@
     dest: "/home/{{ pulsar.user_name }}/Miniconda3-py39_{{ miniconda_version }}-1-Linux-x86_64.sh"
   become: yes
   become_user: "{{ pulsar.user_name }}"
-  when: not miniconda_exists.stat.exists and install_nfs_conda
+  when: not miniconda_exists.stat.exists and csnt_install_nfs_conda
 - name: Install Miniconda to NFS home
   ansible.builtin.shell:
     cmd: "/bin/bash /home/{{ pulsar.user_name }}/Miniconda3-py39_{{ miniconda_version }}-1-Linux-x86_64.sh -b -p {{ miniconda_prefix }}"
   become: yes
   become_user: "{{ pulsar.user_name }}"
-  when: not miniconda_exists.stat.exists and install_nfs_conda
+  when: not miniconda_exists.stat.exists and csnt_install_nfs_conda
 - name: Ensure conda folder is executable
   ansible.builtin.file:
     path: "{{ miniconda_prefix }}/bin"
@@ -87,7 +87,7 @@
     mode: 'a+x'
   become: yes
   become_user: "{{ pulsar.user_name }}"
-  when: install_nfs_conda
+  when: csnt_install_nfs_conda
 - name: Check for mamba bin
   stat:
     path: "{{ miniconda_prefix }}/bin/mamba"
@@ -98,7 +98,7 @@
   ansible.builtin.command: "{{ miniconda_prefix }}/bin/conda install -y -c conda-forge mamba"
   become: yes
   become_user: "{{ pulsar.user_name }}"
-  when: not mamba_exists.stat.exists and install_nfs_conda
+  when: not mamba_exists.stat.exists and csnt_install_nfs_conda
 - name: Ensure conda folder is executable again
   ansible.builtin.file:
     path: "{{ miniconda_prefix }}/bin"
@@ -107,5 +107,4 @@
     mode: 'a+x'
   become: yes
   become_user: "{{ pulsar.user_name }}"
-  when: not mamba_exists.stat.exists and install_nfs_conda
-
+  when: not mamba_exists.stat.exists and csnt_install_nfs_conda