diff --git a/files/galaxy/config/user_preferences_extra_conf.yml b/files/galaxy/config/user_preferences_extra_conf.yml index 60709b238..f5c03bd8b 100644 --- a/files/galaxy/config/user_preferences_extra_conf.yml +++ b/files/galaxy/config/user_preferences_extra_conf.yml @@ -55,7 +55,8 @@ preferences: # - ["Freiburg (Germany) - Condor cluster using Singularity with Conda", condor_singularity_with_conda] # - ["Joint remote GPU cluster using docker engine - Galaxy will decide where to put your job", remote_condor_cluster_gpu_docker] # - ["Joint remote CPU cluster using singularity engine - Galaxy will decide where to put your job", remote_condor_cluster_singularity] - - ["Freiburg (Germany) - Mira's test Pulsar", mira-pulsar] + # - ["Freiburg (Germany) - Mira's test Pulsar", mira-pulsar] + - ["Freiburg (Germany) - bwForCluster NEMO 2", nemo-pulsar] # - ["Freiburg (Germany) - de.NBI cloud - docker", remote_cluster_mq_docker_de01] #- ["Freiburg (Germany) - de.NBI cloud - singularity, 2wd true", remote_cluster_mq_singularity_2wdtrue_de01] # - ["Tübingen (Germany) - de.NBI cloud", remote_cluster_mq_de02] diff --git a/files/galaxy/tpv/destinations.yml.j2 b/files/galaxy/tpv/destinations.yml.j2 index 1a46a6166..6617d8fea 100644 --- a/files/galaxy/tpv/destinations.yml.j2 +++ b/files/galaxy/tpv/destinations.yml.j2 @@ -450,6 +450,34 @@ destinations: require: - ufz-eve-pulsar + pulsar_nemo_tpv: + inherits: pulsar_default + runner: pulsar_eu_nemo + max_accepted_cores: 16 + max_accepted_mem: 64 + min_accepted_gpus: 0 + max_accepted_gpus: 0 + env: + LC_ALL: C + SINGULARITY_CACHEDIR: /home/fr/fr_ds722/pulsar/container_cache + TMP: $_GALAXY_JOB_TMP_DIR + TEMP: $_GALAXY_JOB_TMP_DIR + TMPDIR: $_GALAXY_JOB_TMP_DIR + params: + jobs_directory: /home/fr/fr_ds722/pulsar/jobs_directory + singularity_enabled: true + singularity_command: apptainer + singularity_volumes: "$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/cvmfs/data.galaxyproject.org:ro" + singularity_default_container_id: "/cvmfs/singularity.galaxyproject.org/all/perl:5.26" + container_resolvers: + - type: explicit_singularity + - type: cached_mulled_singularity + cache_directory: /cvmfs/singularity.galaxyproject.org/all/ + cache_directory_cacher_type: dir_mtime + scheduling: + require: + - nemo-pulsar + ############################# # LOCAL CONDOR DESTINATIONS # ############################# diff --git a/templates/galaxy/config/job_conf.yml b/templates/galaxy/config/job_conf.yml index c962b9d70..8277f8eff 100644 --- a/templates/galaxy/config/job_conf.yml +++ b/templates/galaxy/config/job_conf.yml @@ -250,8 +250,15 @@ galaxy_jobconf: amqp_consumer_timeout: 2.0 amqp_publish_retry: "true" amqp_publish_retry_max_retries: 60 + - id: pulsar_eu_nemo + load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner + params: + relay_url: "{{ pulsar_nemo_relay_url }}" + relay_username: "{{ pulsar_nemo_relay_username }}" + relay_password: "{{ pulsar_nemo_relay_password }}" + galaxy_url: "https://usegalaxy.eu" + - default_destination: tpv_dispatcher destinations: - id: local