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 97202f0b..00000000 --- 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/config/tool_conf.xml b/files/galaxy-umsa.grid.cesnet.cz/config/tool_conf.xml index 4664a9e8..8a63fcc4 100644 --- a/files/galaxy-umsa.grid.cesnet.cz/config/tool_conf.xml +++ b/files/galaxy-umsa.grid.cesnet.cz/config/tool_conf.xml @@ -3,41 +3,22 @@
-
- - +
+ + + + + + @@ -49,6 +30,7 @@ +
@@ -80,77 +62,18 @@ -
- - - -
-
-
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 0504b397..dd319846 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/config/tool_conf.xml b/files/galaxy/config/tool_conf.xml index 1d37bba0..7729884d 100644 --- a/files/galaxy/config/tool_conf.xml +++ b/files/galaxy/config/tool_conf.xml @@ -28,16 +28,22 @@
- - + +
+ + + + + + @@ -49,6 +55,7 @@ +
@@ -134,20 +141,12 @@ - - - -
-
-
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 fc06b427..525c9788 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 525c9788..9e60dec0 100644 --- a/files/usegalaxy.cz/tpv_rules_local.yml +++ b/files/usegalaxy.cz/tpv_rules_local.yml @@ -1,2 +1,70 @@ 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,$SCRATCHDIR,/scratch.ssd/galaxyeu/permanent/rosettafold_data/bfd:/opt/RoseTTAFold2/bfd,/scratch.ssd/galaxyeu/permanent/rosettafold_data/pdb100_2021Mar03:/opt/RoseTTAFold2/pdb100_2021Mar03,/scratch.ssd/galaxyeu/permanent/rosettafold_data/UniRef30_2020_06:/opt/RoseTTAFold2/UniRef30_2020_06,/scratch.ssd/galaxyeu/permanent/rosettafold_data/weights:/opt/RoseTTAFold2/network/weights' + singularity_default_container_id: "/cvmfs/singularity.metacentrum.cz/RoseTTAFold2/rosettafold_image.sif" + scheduling: + require: + - singularity + tpv_pulsar_alphafold: + inherits: tpv_pulsar + max_accepted_gpus: 1 + max_gpus: 1 + runner: pulsar_tpv_runner + params: + singularity_run_extra_arguments: '--nv' + singularity_volumes: '$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,$SCRATCHDIR,$ALPHAFOLD_DB:/data/2.3:ro' + submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb:ngpus={int(gpus)}:gpu_mem={int(gpu_mem)}gb -l walltime={int(walltime)}:00:00 -q {{ pulsar.pbs_gpu_queue }} -N {{ pulsar.nfs_prefix }}_j{job.id}__{tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]}__{user.username if user and hasattr(user, 'username') else 'anonymous'}" + scheduling: + require: + - alphafold +tools: + testing_rosettafold2: + cores: 8 + mem: 64 + gpus: 1 + context: + walltime: 24 + scratch: 25 + gpu_mem: 16 + scheduling: + require: + - rosettafold + rosettafold2: + inherits: testing_rosettafold2 + scheduling: + require: + - singularity + toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold/.*: + cores: 8 + mem: 120 + gpus: 1 + context: + walltime: 24 + scratch: 100 + gpu_mem: 16 + env: + MPLCONFIGDIR: "$SCRATCHDIR" + ALPHAFOLD_DB: "/scratch.ssd/galaxyeu/permanent/alphafold.db" + ALPHAFOLD_USE_GPU: True + scheduling: + require: + - alphafold diff --git a/group_vars/galaxyservers.yml b/group_vars/galaxyservers.yml index e9da4d92..86784478 100644 --- a/group_vars/galaxyservers.yml +++ b/group_vars/galaxyservers.yml @@ -270,6 +270,11 @@ galaxy_config_templates: - src: "{{ lookup('first_found', ['templates/'+inventory_hostname+'/config/file_source_templates.yml.j2', 'templates/galaxy/config/file_source_templates.yml.j2']) }}" dest: "{{ galaxy_config_dir }}/file_source_templates.yml" +galaxy_local_tools: + - testing.xml + - testing_pbs.xml + - testing_html.xml + galaxy_extra_dirs: - "{{ tpv_config_dir }}" - "{{ galaxy_config_dir }}/plugins/activities" 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 aaaf92cb..d27d1962 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 @@ -21,7 +21,7 @@ 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 4ed0dfe9..b8b804e3 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 @@ -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: 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 d1c2920c..b4dbd0ce 100644 --- a/host_vars/galaxy-umsa.grid.cesnet.cz/vars.yml +++ b/host_vars/galaxy-umsa.grid.cesnet.cz/vars.yml @@ -32,7 +32,7 @@ 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 f11e57b0..5e714027 100644 --- a/host_vars/usegalaxy.cz/vars.yml +++ b/host_vars/usegalaxy.cz/vars.yml @@ -27,7 +27,7 @@ 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" @@ -39,3 +39,10 @@ galaxy_config_files: dest: "{{ galaxy_config_dir }}/file_sources_conf.yml" - src: files/{{ inventory_hostname }}/user_preferences_extra_conf.yml dest: "{{ galaxy_config_dir }}/user_preferences_extra_conf.yml" + +galaxy_local_tools: + - testing.xml + - testing_pbs.xml + - testing_html.xml + - rosettafold2.xml + - rosettafold2_sing.xml diff --git a/templates/galaxy-qa1.galaxy.cloud.e-infra.cz/config/local_tool_conf.xml.j2 b/templates/galaxy-qa1.galaxy.cloud.e-infra.cz/config/local_tool_conf.xml.j2 index 084bcb35..7f54acdd 100644 --- a/templates/galaxy-qa1.galaxy.cloud.e-infra.cz/config/local_tool_conf.xml.j2 +++ b/templates/galaxy-qa1.galaxy.cloud.e-infra.cz/config/local_tool_conf.xml.j2 @@ -2,4 +2,5 @@ + diff --git a/templates/galaxy-qa2.galaxy.cloud.e-infra.cz/config/local_tool_conf.xml.j2 b/templates/galaxy-qa2.galaxy.cloud.e-infra.cz/config/local_tool_conf.xml.j2 index 084bcb35..7f54acdd 100644 --- a/templates/galaxy-qa2.galaxy.cloud.e-infra.cz/config/local_tool_conf.xml.j2 +++ b/templates/galaxy-qa2.galaxy.cloud.e-infra.cz/config/local_tool_conf.xml.j2 @@ -2,4 +2,5 @@ + diff --git a/templates/galaxy-umsa.grid.cesnet.cz/config/local_tool_conf.xml.j2 b/templates/galaxy-umsa.grid.cesnet.cz/config/local_tool_conf.xml.j2 index d7cf9777..b59ba5d2 100644 --- a/templates/galaxy-umsa.grid.cesnet.cz/config/local_tool_conf.xml.j2 +++ b/templates/galaxy-umsa.grid.cesnet.cz/config/local_tool_conf.xml.j2 @@ -3,5 +3,6 @@
diff --git a/templates/galaxy/config/tpv_rules_meta.yml.j2 b/templates/galaxy/config/tpv_rules_meta.yml.j2 index 797f91cc..82dd2d82 100644 --- a/templates/galaxy/config/tpv_rules_meta.yml.j2 +++ b/templates/galaxy/config/tpv_rules_meta.yml.j2 @@ -1,6 +1,5 @@ global: default_inherits: default - tools: default: cores: 1 @@ -20,10 +19,10 @@ tools: - pulsar reject: - offline + - docker rules: [] rank: | helpers.weighted_random_sampling(candidate_destinations) - local_running_tools: abstract: True scheduling: @@ -31,32 +30,12 @@ tools: - local reject: - pulsar - local_sing_running_tools: inherits: local_running_tools abstract: True scheduling: require: - singularity - - testing_rosettafold2: - cores: 8 - mem: 64 - gpus: 1 - context: - walltime: 24 - scratch: 25 - gpu_mem: 16 - scheduling: - require: - - rosettafold - - rosettafold2: - inherits: testing_rosettafold2 - scheduling: - require: - - singularity - .*testing.*: cores: 1 mem: 1 @@ -70,7 +49,6 @@ tools: # last line in block must evaluate to a value - which determines whether the TPV if conditional matches or not not user or (user.email not in admin_users and user.email not in ['galaxy@cesnet.cz','galaxy@usegalaxy.cz']) fail: Unauthorized. Only admins can execute this tool. - - id: resource_params_defined if: | param_dict = job.get_param_values(app) @@ -78,65 +56,39 @@ tools: cores: int(job.get_param_values(app)['__job_resource']['cores']) context: walltime: "{int(job.get_param_values(app)['__job_resource']['time'])}" - - .*/alphafold/.*: - cores: 8 - mem: 120 - gpus: 1 - context: - walltime: 24 - scratch: 100 - gpu_mem: 16 - env: - MPLCONFIGDIR: "$SCRATCHDIR" - ALPHAFOLD_DB: "/scratch.ssd/galaxyeu/permanent/alphafold.db" - ALPHAFOLD_USE_GPU: True - scheduling: - require: - - alphafold - - .*/goenrichment/.*: - scheduling: - require: - - nasty-java - - .*/bedtools_annotatebed/.*: + toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/.*: context: walltime: 48 - - .*/megahit/.*: + toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/.*: cores: 16 mem: 256 context: walltime: 96 scratch: 100 - - .*/hapog/.*: + toolshed.g2.bx.psu.edu/repos/iuc/hapog/hapog/.*: cores: 8 context: walltime: 48 - __SET_.*: inherits: local_running_tools - __IMPORT_HISTORY__: inherits: local_running_tools - __EXPORT_HISTORY__: inherits: local_running_tools - - "Show .*": + "Show beginning1": + inherits: local_running_tools + "Show tail1": inherits: local_running_tools - - "Remove .*": + "Remove beginning1": inherits: local_running_tools - cat1: inherits: local_running_tools - .*/data_manager_.*: inherits: local_sing_running_tools - + toolshed.g2.bx.psu.edu/repos/iuc/goenrichment/goenrichment/2.0.1/.*: + scheduling: + require: + - nasty-java roles: training.*: max_cores: 4 @@ -145,7 +97,6 @@ roles: require: - pulsar - training - destinations: tpv_local: runner: local_runner @@ -218,53 +169,17 @@ destinations: scheduling: require: - pulsar - tpv_pulsar_nasty_java: - inherits: tpv_pulsar - runner: pulsar_tpv_runner - params: - singularity_run_extra_arguments: '--env _JAVA_OPTIONS="-Xmx{int(mem)}g -Djava.io.tmpdir=$SCRATCHDIR"' - scheduling: - require: - - nasty-java - tpv_pulsar_alphafold: - inherits: tpv_pulsar - max_accepted_gpus: 1 - max_gpus: 1 - runner: pulsar_tpv_runner - params: - singularity_run_extra_arguments: '--nv' - singularity_volumes: '$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,$SCRATCHDIR,$ALPHAFOLD_DB:/data/2.3:ro' - 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 {{ pulsar.pbs_gpu_queue }} -N {{ pulsar.nfs_prefix }}_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: - - alphafold tpv_pulsar_training: inherits: tpv_pulsar runner: pulsar_tpv_runner scheduling: require: - training -# usegalaxy.cz specific: - tpv_pulsar_rosettafold: + tpv_pulsar_nasty_java: 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,$SCRATCHDIR,/scratch.ssd/galaxyeu/permanent/rosettafold_data/bfd:/opt/RoseTTAFold2/bfd,/scratch.ssd/galaxyeu/permanent/rosettafold_data/pdb100_2021Mar03:/opt/RoseTTAFold2/pdb100_2021Mar03,/scratch.ssd/galaxyeu/permanent/rosettafold_data/UniRef30_2020_06:/opt/RoseTTAFold2/UniRef30_2020_06,/scratch.ssd/galaxyeu/permanent/rosettafold_data/weights:/opt/RoseTTAFold2/network/weights' - singularity_default_container_id: "/cvmfs/singularity.metacentrum.cz/RoseTTAFold2/rosettafold_image.sif" + singularity_run_extra_arguments: '--env _JAVA_OPTIONS="-Xmx{int(mem)}g -Djava.io.tmpdir=$SCRATCHDIR"' scheduling: require: - - singularity + - nasty-java diff --git a/templates/usegalaxy.cz/config/local_tool_conf.xml.j2 b/templates/usegalaxy.cz/config/local_tool_conf.xml.j2 index f2bcad3a..df08bdfa 100644 --- a/templates/usegalaxy.cz/config/local_tool_conf.xml.j2 +++ b/templates/usegalaxy.cz/config/local_tool_conf.xml.j2 @@ -3,6 +3,7 @@