diff --git a/files/galaxy-qa1.galaxy.cloud.e-infra.cz/tpv_rules_local.yml b/files/galaxy-qa1.galaxy.cloud.e-infra.cz/tpv_rules_local.yml deleted file mode 100644 index 97202f0..0000000 --- a/files/galaxy-qa1.galaxy.cloud.e-infra.cz/tpv_rules_local.yml +++ /dev/null @@ -1,5 +0,0 @@ -# empty intentionally - -# prevent tpv lint complaints -global: - default_inherits: default diff --git a/files/galaxy-umsa.grid.cesnet.cz/tpv_rules_local.yml b/files/galaxy-umsa.grid.cesnet.cz/tpv_rules_local.yml index 0504b39..dd31984 100644 --- a/files/galaxy-umsa.grid.cesnet.cz/tpv_rules_local.yml +++ b/files/galaxy-umsa.grid.cesnet.cz/tpv_rules_local.yml @@ -44,6 +44,6 @@ tools: mem: 16 .*/fastqc/.*: - cores: 1 + cores: 1 context: walltime: 2 diff --git a/files/galaxy-qa2.galaxy.cloud.e-infra.cz/tpv_rules_local.yml b/files/galaxy/config/tpv_rules_local.yml similarity index 54% rename from files/galaxy-qa2.galaxy.cloud.e-infra.cz/tpv_rules_local.yml rename to files/galaxy/config/tpv_rules_local.yml index fc06b42..525c978 100644 --- a/files/galaxy-qa2.galaxy.cloud.e-infra.cz/tpv_rules_local.yml +++ b/files/galaxy/config/tpv_rules_local.yml @@ -1,3 +1,2 @@ -# prevent tpv lint complaints global: default_inherits: default diff --git a/files/usegalaxy.cz/tpv_rules_local.yml b/files/usegalaxy.cz/tpv_rules_local.yml index 525c978..d127570 100644 --- a/files/usegalaxy.cz/tpv_rules_local.yml +++ b/files/usegalaxy.cz/tpv_rules_local.yml @@ -1,2 +1,26 @@ global: default_inherits: default +destinations: + tpv_pulsar_rosettafold: + inherits: tpv_pulsar + runner: pulsar_tpv_runner + params: + singularity_enabled: false + submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb:ngpus={int(gpus)}:gpu_mem={int(gpu_mem)}gb -l walltime={int(walltime)}:00:00 -q galaxy_gpu@pbs-m1.metacentrum.cz -N pulsar_cz_j{job.id}__{tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]}__{user.username if user and hasattr(user, 'username') else 'anonymous'}" + scheduling: + require: + - rosettafold + tpv_pulsar_rosettafold_sing: + inherits: tpv_pulsar_rosettafold + container_resolvers: + - type: explicit_singularity + - cache_directory: /cvmfs/singularity.metacentrum.cz/RoseTTAFold2/ + type: cached_mulled_singularity + params: + singularity_enabled: true + singularity_run_extra_arguments: '--nv --env SCRATCHDIR="$SCRATCHDIR" --env SCRATCH=$SCRATCHDIR' + singularity_volumes: '$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,$SCRATCHDIR,/scratch.ssd/galaxyeu/permanent/rosettafold_data/bfd:/opt/RoseTTAFold2/bfd,/scratch.ssd/galaxyeu/permanent/rosettafold_data/pdb100_2021Mar03:/opt/RoseTTAFold2/pdb100_2021Mar03,/scratch.ssd/galaxyeu/permanent/rosettafold_data/UniRef30_2020_06:/opt/RoseTTAFold2/UniRef30_2020_06,/scratch.ssd/galaxyeu/permanent/rosettafold_data/weights:/opt/RoseTTAFold2/network/weights' + singularity_default_container_id: "/cvmfs/singularity.metacentrum.cz/RoseTTAFold2/rosettafold_image.sif" + scheduling: + require: + - singularity diff --git a/host_vars/galaxy-qa1.galaxy.cloud.e-infra.cz/vars.yml b/host_vars/galaxy-qa1.galaxy.cloud.e-infra.cz/vars.yml index 2781a39..c4f9c0d 100644 --- a/host_vars/galaxy-qa1.galaxy.cloud.e-infra.cz/vars.yml +++ b/host_vars/galaxy-qa1.galaxy.cloud.e-infra.cz/vars.yml @@ -17,7 +17,7 @@ pulsar: galaxy_config_files: - src: files/galaxy/themes.yml dest: "{{ galaxy_config.galaxy.themes_config_file }}" - - src: "files/{{ inventory_hostname }}/tpv_rules_local.yml" + - src: "{{ lookup('first_found', ['files/'+inventory_hostname+'/tpv_rules_local.yml', 'files/galaxy/config/tpv_rules_local.yml']) }}" dest: "{{ tpv_mutable_dir }}/tpv_rules_{{ inventory_hostname }}.yml" - src: "{{ lookup('first_found', ['files/'+inventory_hostname+'/config/tool_conf.xml', 'files/galaxy/config/tool_conf.xml']) }}" dest: "{{ galaxy_config_dir }}/tool_conf.xml" diff --git a/host_vars/galaxy-qa2.galaxy.cloud.e-infra.cz/vars.yml b/host_vars/galaxy-qa2.galaxy.cloud.e-infra.cz/vars.yml index 72a8d6a..e6f54e8 100644 --- a/host_vars/galaxy-qa2.galaxy.cloud.e-infra.cz/vars.yml +++ b/host_vars/galaxy-qa2.galaxy.cloud.e-infra.cz/vars.yml @@ -16,7 +16,7 @@ pulsar: galaxy_config_files: - src: files/galaxy/themes.yml dest: "{{ galaxy_config.galaxy.themes_config_file }}" - - src: "files/{{ inventory_hostname }}/tpv_rules_local.yml" + - src: "{{ lookup('first_found', ['files/'+inventory_hostname+'/tpv_rules_local.yml', 'files/galaxy/config/tpv_rules_local.yml']) }}" dest: "{{ tpv_mutable_dir }}/tpv_rules_{{ inventory_hostname }}.yml" - src: files/{{ inventory_hostname }}/file_sources_conf.yml dest: "{{ galaxy_config_dir }}/file_sources_conf.yml" diff --git a/host_vars/galaxy-umsa.grid.cesnet.cz/vars.yml b/host_vars/galaxy-umsa.grid.cesnet.cz/vars.yml index 851108b..2f9a6c9 100644 --- a/host_vars/galaxy-umsa.grid.cesnet.cz/vars.yml +++ b/host_vars/galaxy-umsa.grid.cesnet.cz/vars.yml @@ -31,7 +31,7 @@ pulsar: galaxy_config_files: - src: files/galaxy/themes.yml dest: "{{ galaxy_config.galaxy.themes_config_file }}" - - src: "files/{{ inventory_hostname }}/tpv_rules_local.yml" + - src: "{{ lookup('first_found', ['files/'+inventory_hostname+'/tpv_rules_local.yml', 'files/galaxy/config/tpv_rules_local.yml']) }}" dest: "{{ tpv_mutable_dir }}/tpv_rules_{{ inventory_hostname }}.yml" - src: "{{ lookup('first_found', ['files/'+inventory_hostname+'/config/tool_conf.xml', 'files/galaxy/config/tool_conf.xml']) }}" dest: "{{ galaxy_config_dir }}/tool_conf.xml" diff --git a/host_vars/usegalaxy.cz/vars.yml b/host_vars/usegalaxy.cz/vars.yml index 1cd825a..4d870f5 100644 --- a/host_vars/usegalaxy.cz/vars.yml +++ b/host_vars/usegalaxy.cz/vars.yml @@ -26,7 +26,7 @@ pulsar: galaxy_config_files: - src: files/galaxy/themes.yml dest: "{{ galaxy_config.galaxy.themes_config_file }}" - - src: "files/{{ inventory_hostname }}/tpv_rules_local.yml" + - src: "{{ lookup('first_found', ['files/'+inventory_hostname+'/tpv_rules_local.yml', 'files/galaxy/config/tpv_rules_local.yml']) }}" dest: "{{ tpv_mutable_dir }}/tpv_rules_{{ inventory_hostname }}.yml" - src: "{{ lookup('first_found', ['files/'+inventory_hostname+'/config/tool_conf.xml', 'files/galaxy/config/tool_conf.xml']) }}" dest: "{{ galaxy_config_dir }}/tool_conf.xml" diff --git a/templates/galaxy/config/tpv_rules_meta.yml.j2 b/templates/galaxy/config/tpv_rules_meta.yml.j2 index 7f60a51..b7f9379 100644 --- a/templates/galaxy/config/tpv_rules_meta.yml.j2 +++ b/templates/galaxy/config/tpv_rules_meta.yml.j2 @@ -18,6 +18,7 @@ tools: - pulsar reject: - offline + - docker rules: [] rank: | helpers.weighted_random_sampling(candidate_destinations) @@ -43,15 +44,15 @@ tools: gpus: 1 context: walltime: 24 - scratch: 25 + scratch: 25 gpu_mem: 16 - scheduling: + scheduling: require: - rosettafold rosettafold2: inherits: testing_rosettafold2 - scheduling: + scheduling: require: - singularity @@ -234,27 +235,3 @@ destinations: scheduling: require: - training -# usegalaxy.cz specific: - tpv_pulsar_rosettafold: - inherits: tpv_pulsar - runner: pulsar_tpv_runner - params: - singularity_enabled: false - submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb:ngpus={int(gpus)}:gpu_mem={int(gpu_mem)}gb -l walltime={int(walltime)}:00:00 -q galaxy_gpu@pbs-m1.metacentrum.cz -N pulsar_cz_j{job.id}__{tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]}__{user.username if user and hasattr(user, 'username') else 'anonymous'}" - scheduling: - require: - - rosettafold - tpv_pulsar_rosettafold_sing: - inherits: tpv_pulsar_rosettafold - container_resolvers: - - type: explicit_singularity - - cache_directory: /cvmfs/singularity.metacentrum.cz/RoseTTAFold2/ - type: cached_mulled_singularity - params: - singularity_enabled: true - singularity_run_extra_arguments: '--nv --env SCRATCHDIR="$SCRATCHDIR" --env SCRATCH=$SCRATCHDIR' - singularity_volumes: '$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,$SCRATCHDIR,/scratch.ssd/galaxyeu/permanent/rosettafold_data/bfd:/opt/RoseTTAFold2/bfd,/scratch.ssd/galaxyeu/permanent/rosettafold_data/pdb100_2021Mar03:/opt/RoseTTAFold2/pdb100_2021Mar03,/scratch.ssd/galaxyeu/permanent/rosettafold_data/UniRef30_2020_06:/opt/RoseTTAFold2/UniRef30_2020_06,/scratch.ssd/galaxyeu/permanent/rosettafold_data/weights:/opt/RoseTTAFold2/network/weights' - singularity_default_container_id: "/cvmfs/singularity.metacentrum.cz/RoseTTAFold2/rosettafold_image.sif" - scheduling: - require: - - singularity