diff --git a/files/galaxy-gxit.grid.cesnet.cz/cert.pem b/files/galaxy-gxit.grid.cesnet.cz/cert.pem deleted file mode 100644 index 64fac63..0000000 --- a/files/galaxy-gxit.grid.cesnet.cz/cert.pem +++ /dev/null @@ -1,83 +0,0 @@ ------BEGIN CERTIFICATE----- -MIIH1DCCBbygAwIBAgIQQMXk7KTGbZpJCmmAzCmWozANBgkqhkiG9w0BAQwFADBE -MQswCQYDVQQGEwJOTDEZMBcGA1UEChMQR0VBTlQgVmVyZW5pZ2luZzEaMBgGA1UE -AxMRR0VBTlQgT1YgUlNBIENBIDQwHhcNMjMxMTA2MDAwMDAwWhcNMjQxMTA1MjM1 -OTU5WjCBjDELMAkGA1UEBhMCQ1oxHjAcBgNVBAgMFVByYWhhLCBIbGF2bsOtIG3E -m3N0bzE4MDYGA1UECgwvQ0VTTkVULCB6w6FqbW92w6kgc2RydcW+ZW7DrSBwcsOh -dm5pY2vDvWNoIG9zb2IxIzAhBgNVBAMTGmdhbGF4eS1neGl0LmdyaWQuY2VzbmV0 -LmN6MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAlervnoeuT6a0bhx6 -2BoCiyOpzmGVzwE9FrdxBYKjL3W/xcJiKUxZ/09xMJJK7fxv60AgnuCNk2OOokUx -fwnRfxcAaKw49HKzX0ByGjK1rfalUkFvHucGivDssoAqL00oCyNep1Ci54qKqDbN -3+UDGCmz85fRDO5WfhlfUucAt0eGYWw8PXLYP4cYSDSRjVPsUdxSLKXQlFFZ31iA -SLtjvwfeh7P3S3sVtGbL9x9o/UQCP6l/clVp4/4m1Atf2lHiDAq6swg9pG4RnQhO 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revisions: - - 983bf725dfc2 - tool_panel_section_label: Get Data - tool_shed_url: toolshed.g2.bx.psu.edu -- name: sra_tools - owner: iuc - revisions: - - 734abc7ac21d - - f5ea3ce9b9b0 - tool_panel_section_label: Get Data - tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/files/galaxy-gxit.grid.cesnet.cz/tpv_rules_local.yml b/files/galaxy-gxit.grid.cesnet.cz/tpv_rules_local.yml deleted file mode 100644 index b8cbc32..0000000 --- a/files/galaxy-gxit.grid.cesnet.cz/tpv_rules_local.yml +++ /dev/null @@ -1,6 +0,0 @@ -# empty intentionally - -# prevent tpv lint complaints -global: - default_inherits: default - diff --git a/files/usegalaxy-test.cerit-sc.cz/pulsar.pub b/files/usegalaxy-test.cerit-sc.cz/pulsar.pub deleted file mode 100644 index f632515..0000000 --- a/files/usegalaxy-test.cerit-sc.cz/pulsar.pub +++ /dev/null @@ -1 +0,0 @@ -ssh-rsa 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revisions: - - 983bf725dfc2 - tool_panel_section_label: Get Data - tool_shed_url: toolshed.g2.bx.psu.edu -- name: sra_tools - owner: iuc - revisions: - - 734abc7ac21d - - f5ea3ce9b9b0 - tool_panel_section_label: Get Data - tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/files/usegalaxy-test.cerit-sc.cz/tpv_rules_local.yml b/files/usegalaxy-test.cerit-sc.cz/tpv_rules_local.yml deleted file mode 100644 index b8cbc32..0000000 --- a/files/usegalaxy-test.cerit-sc.cz/tpv_rules_local.yml +++ /dev/null @@ -1,6 +0,0 @@ -# empty intentionally - -# prevent tpv lint complaints -global: - default_inherits: default - diff --git a/files/usegalaxy.cz/tool_list.yaml b/files/usegalaxy.cz/tool_list.yaml index c60ab30..6240c65 100644 --- a/files/usegalaxy.cz/tool_list.yaml +++ b/files/usegalaxy.cz/tool_list.yaml @@ -1,15622 +1,19 @@ tools: -- name: iedb_api - owner: iuc - revisions: - - 7ed6dda64a81 - 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: sra_tools - owner: iuc - revisions: - - 734abc7ac21d - - 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: spocc_occ - owner: ecology - revisions: - - f64b3c1a80a6 - 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: 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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 +- name: fastqc owner: devteam revisions: - - 7b1b03c4465d - tool_panel_section_label: Metagenomic Analysis + - 5ec9f6bceaee + tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu -- name: find_diag_hits +- name: bwa owner: devteam revisions: - - acf51ff24c7d - tool_panel_section_label: Metagenomic Analysis + - 2477830927ec + tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu -- name: count_covariates - owner: devteam +- name: alphafold2 + owner: galaxy-australia revisions: - - 14e304b70425 - tool_panel_section_label: GATK Tools + - 3f188450ca4f + tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/files/usegalaxy.cz/tpv_rules_local.yml b/files/usegalaxy.cz/tpv_rules_local.yml index 353e3af..525c978 100644 --- a/files/usegalaxy.cz/tpv_rules_local.yml +++ b/files/usegalaxy.cz/tpv_rules_local.yml @@ -1,46 +1,2 @@ global: default_inherits: default - -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 - -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,$SCRATCHDIR,/scratch.ssd/galaxyeu/permanent/rosettafold_data/bfd:/opt/RoseTTAFold2/bfd,/scratch.ssd/galaxyeu/permanent/rosettafold_data/pdb100_2021Mar03:/opt/RoseTTAFold2/pdb100_2021Mar03,/scratch.ssd/galaxyeu/permanent/rosettafold_data/UniRef30_2020_06:/opt/RoseTTAFold2/UniRef30_2020_06,/scratch.ssd/galaxyeu/permanent/rosettafold_data/weights:/opt/RoseTTAFold2/network/weights' - singularity_default_container_id: "/cvmfs/singularity.metacentrum.cz/RoseTTAFold2/rosettafold_image.sif" - scheduling: - require: - - singularity diff --git a/group_vars/galaxyservers.yml b/group_vars/galaxyservers.yml index 7a64524..ee7e108 100644 --- a/group_vars/galaxyservers.yml +++ b/group_vars/galaxyservers.yml @@ -178,7 +178,7 @@ galaxy_config: virtualenv: "{{ galaxy_venv_dir }}" gunicorn: # listening options - bind: "unix:{{ galaxy_mutable_config_dir }}/gunicorn.sock" + bind: "unix:{{ galaxy_root }}/var/gunicorn.sock" # performance options workers: 2 # Other options that will be passed to gunicorn @@ -207,9 +207,9 @@ galaxy_config: - job-handlers - workflow-schedulers reports: - enable: true + enable: false url_prefix: /reports - bind: "unix:{{ galaxy_mutable_config_dir }}/reports.sock" + bind: "unix:{{ galaxy_root }}/var/reports.sock" config_file: "{{ galaxy_config_dir }}/reports.yml" galaxy_job_config_file: "{{ galaxy_config_dir }}/galaxy.yml" @@ -336,6 +336,8 @@ rabbitmq_plugins: rabbitmq_conf_ssl_certificate: /etc/ssl/certs/fullchain.pem rabbitmq_conf_ssl_certificate_key: /etc/ssl/user/privkey-999:999.pem +rabbitmq_container_pause: 60 + rabbitmq_config: listeners: tcp: none diff --git a/host_vars/galaxy-gxit.grid.cesnet.cz/secret.yml b/host_vars/galaxy-gxit.grid.cesnet.cz/secret.yml deleted file mode 100644 index f08f509..0000000 --- a/host_vars/galaxy-gxit.grid.cesnet.cz/secret.yml +++ /dev/null @@ -1,264 +0,0 @@ -$ANSIBLE_VAULT;1.1;AES256 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dcd341f..0000000 --- a/host_vars/galaxy-gxit.grid.cesnet.cz/vars.yml +++ /dev/null @@ -1,26 +0,0 @@ -# where to put most of the data; we use RBD or NBD volumes -galaxy_mutable_data_dir: /data/galaxy - -enable_flower: no -enable_telegraf: no - - -pulsar: - user_name: galaxyelixir - nfs_home: brno11-elixir - nfs_prefix: pulsar-gxit - pbs_queue: galaxyre - pbs_gpu_queue: galaxy_gpu - -pulsar_data_dir: "/storage/{{ pulsar.nfs_home }}/home/{{ pulsar.user_name }}/{{ pulsar.nfs_prefix }}" - -copy_tools_from: usegalaxy.eu - -# just test -#extra_certbot_domains: -# - "nonexistent.domain" - -admin_ssh_keys: | - ssh-rsa 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 ljocha@abiff - ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQCscnBHx46RNH0xgJGFQDuRvcjsf+0KE4lHMZuxhY3z70/kR3oJFZ0ns6/26QGCmhKVlSePKIO8idC1U5hqDXqhRB+Kpx/4yDcUNMtU4Xklmfqqv47uyq6/oylNjJgAbD691K21SZQSGP8nEz2LZlB3d9eNx131mVfMegyyQnnSLXqvQn1PGpwq9yCeV7RstAI67dL+ilglFWIUwkmwr7V6AKSPwYgFZE/uZJ0qfZ6+PBhS6+/zsDcq1N9OhtsHNsM1esglvWwu5zW83uuqB2p2FaG/Aoy3+70vDiwhjvgiXor/2jOx4Vzfv1c/55X8gmsOWT/WmQwoE2ernbFBFc8h ljocha@hiram.ics.muni.cz - ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABgQDAfdMuyDmA84qskMECxjuep3V5tCAwPHYs10Qr5GQFR3wywJuarAVoFj4YR31mcmKR3ZkYRAOKJZepSGm11ojT9n5F+ctMrGhC5RmxlXhDF6RNadfx5QVkkRfldjkR4G+2iCtm4CA9bdSU57jQHtqXyyaw7+NqPiJmq6s+OIqCew6Mick+lCVCgwpbjm6Zg4E3fAYvxKPaB8fClpC+YM+wyBnG6dgq5Qb3qXMVrC0db1xpbQQbt91YWWzG6IAxFO/as1CRw/y4qS+60UlTjBp0umD5iK0ZDqfXI/aQrahOFZXQyobEGaiS1e8qcKEl+mFOxbkQpdXLZIdvgWrw6/LAS6i918lrOFrR/vtn67CP/yFwRqWcgXDRhlafmKL2LpKg61OsuJYP1fD4ccFyl+lTLs6yaR5i6HScbw5qtfWBYjFFdYRpiPw0YEPhFzwFsWRFB/FTxgjgVb0Ek+CWHRPTsRKCVtotUTgsAMO7mDvIre9y0ONkokS65bpGvBVMptk= action@github 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 07b2d01..9493abd 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 @@ -31,8 +31,3 @@ galaxy_config_files: # just test #extra_certbot_domains: # - "nonexistent.domain" - -admin_ssh_keys: | - ssh-rsa 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diff --git a/host_vars/usegalaxy-test.cerit-sc.cz/vars.yml b/host_vars/usegalaxy-test.cerit-sc.cz/vars.yml deleted file mode 100644 index e15e6b2..0000000 --- a/host_vars/usegalaxy-test.cerit-sc.cz/vars.yml +++ /dev/null @@ -1,25 +0,0 @@ -# where to put most of the data; we use RBD or NBD volumes -galaxy_mutable_data_dir: /data/galaxy - -enable_flower: no -enable_telegraf: no - -pulsar: - user_name: galaxyelixir - nfs_home: brno11-elixir - nfs_prefix: pulsar-cz-test - pbs_queue: galaxyre - pbs_gpu_queue: galaxy_gpu - -pulsar_data_dir: "/storage/{{ pulsar.nfs_home }}/home/{{ pulsar.user_name }}/{{ pulsar.nfs_prefix }}" - -copy_tools_from: usegalaxy.eu - -# just test -#extra_certbot_domains: -# - "nonexistent.domain" - -admin_ssh_keys: | - ssh-rsa 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 ljocha@abiff - ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQCscnBHx46RNH0xgJGFQDuRvcjsf+0KE4lHMZuxhY3z70/kR3oJFZ0ns6/26QGCmhKVlSePKIO8idC1U5hqDXqhRB+Kpx/4yDcUNMtU4Xklmfqqv47uyq6/oylNjJgAbD691K21SZQSGP8nEz2LZlB3d9eNx131mVfMegyyQnnSLXqvQn1PGpwq9yCeV7RstAI67dL+ilglFWIUwkmwr7V6AKSPwYgFZE/uZJ0qfZ6+PBhS6+/zsDcq1N9OhtsHNsM1esglvWwu5zW83uuqB2p2FaG/Aoy3+70vDiwhjvgiXor/2jOx4Vzfv1c/55X8gmsOWT/WmQwoE2ernbFBFc8h ljocha@hiram.ics.muni.cz - ssh-rsa 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 action@github diff --git a/host_vars/usegalaxy.cz/secret.yml b/host_vars/usegalaxy.cz/secret.yml index e51eb62..da62af2 100644 --- a/host_vars/usegalaxy.cz/secret.yml +++ b/host_vars/usegalaxy.cz/secret.yml @@ -1,195 +1,195 @@ $ANSIBLE_VAULT;1.1;AES256 -62623833656561656139343564373766376265386337373439306161643737653834303066656662 -3632316561623662666162656564303839626235336536320a303530656562303466643530623731 -66316433353335336362353938633564623635653764653862356364356639343565323763643239 -3761306164303565640a306638313935346561343133343033353833666565646562353463616231 -31373762663838393564643930303237363335303731643036386133356466623435333665303832 -38613334616237623265346365356166393332383361666636363634303366383532393864663334 -30323364356165616564306332323134653363643331323365393035386535323832376437656265 -62616561353637393763343665383366383634616630343764306164303630343436396638326235 -65386539323561303334666361353336626432376138613863356562646435356433313035626233 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diff --git a/host_vars/usegalaxy.cz/vars.yml b/host_vars/usegalaxy.cz/vars.yml index 18cdf69..1377bd3 100644 --- a/host_vars/usegalaxy.cz/vars.yml +++ b/host_vars/usegalaxy.cz/vars.yml @@ -6,10 +6,17 @@ extra_certbot_domains: galaxy_mutable_data_dir: /rbd/data galaxy_commit_id: release_23.0 +galaxy_build_client: false -enable_flower: yes -enable_telegraf: yes +copy_tools_from: usegalaxy.eu +csnt_log_level: DEBUG + +enable_flower: no +enable_telegraf: no + +miniconda_version: 24.11.1 +csnt_short_term_storage_dir: /rbd/data/short_term_web_storage pulsar: user_name: galaxyeu @@ -18,6 +25,8 @@ pulsar: pbs_queue: galaxycz pbs_gpu_queue: galaxy_gpu +pulsar_data_dir: "/storage/{{ pulsar.nfs_home }}/home/{{ pulsar.user_name }}/{{ pulsar.nfs_prefix }}" + galaxy_config_files: - src: files/galaxy/themes.yml dest: "{{ galaxy_config.galaxy.themes_config_file }}" @@ -27,10 +36,3 @@ galaxy_config_files: dest: "{{ galaxy_config.galaxy.tool_config_file[0] }}" - src: files/galaxy/config/oidc_config.xml dest: "{{ galaxy_config_dir }}/oidc_config.xml" - -pulsar_data_dir: "/storage/{{ pulsar.nfs_home }}/home/{{ pulsar.user_name }}/{{ pulsar.nfs_prefix }}" - -copy_tools_from: usegalaxy.eu - -admin_ssh_keys: | - ssh-rsa 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 action@github diff --git a/templates/galaxy/config/tpv_rules_meta.yml.j2 b/templates/galaxy/config/tpv_rules_meta.yml.j2 index 94da284..7fecf60 100644 --- a/templates/galaxy/config/tpv_rules_meta.yml.j2 +++ b/templates/galaxy/config/tpv_rules_meta.yml.j2 @@ -37,6 +37,24 @@ tools: 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 @@ -203,3 +221,27 @@ 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 diff --git a/templates/nginx/galaxy.j2 b/templates/nginx/galaxy.j2 index 9d52d57..5b38414 100644 --- a/templates/nginx/galaxy.j2 +++ b/templates/nginx/galaxy.j2 @@ -103,6 +103,8 @@ server { proxy_set_header X-Forwarded-Proto $scheme; } +{% block flower %} +{% if (enable_flower | default(false) ) %} location /flower { proxy_pass http://localhost:5555; proxy_set_header Host $host; @@ -111,7 +113,10 @@ server { proxy_set_header Upgrade $http_upgrade; proxy_set_header Connection "upgrade"; } - +{% endif %} +{% endblock flower %} +{% block reports %} +{% if (galaxy_config.gravity.reports.enable | default(false) ) %} location /reports/ { auth_basic galaxy; auth_basic_user_file /etc/nginx/passwd; @@ -119,12 +124,16 @@ server { proxy_set_header X-Forwarded-Host $host; proxy_set_header X-Forwarded-Proto $scheme; } - +{% endif %} +{% endblock reports %} +{% block grafana %} +{% if (enable_telegraf | default(false) ) %} location /grafana/ { proxy_pass http://127.0.0.1:3000/; proxy_set_header Host $http_host; } - +{% endif %} +{% endblock grafana %} {{ tiaas_nginx_routes }} }