From 7efcb4da3e43b3f0ef43c9abd71e853f1aefa79a Mon Sep 17 00:00:00 2001 From: Martin Demko <325073@mail.muni.cz> Date: Thu, 17 Apr 2025 12:40:49 +0200 Subject: [PATCH 1/2] Adds proper SINGULARITY_CACHEDIR variables update for singularity resolver. --- templates/galaxy/config/tpv_rules_meta.yml.j2 | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/templates/galaxy/config/tpv_rules_meta.yml.j2 b/templates/galaxy/config/tpv_rules_meta.yml.j2 index 7f60a51..d45ced7 100644 --- a/templates/galaxy/config/tpv_rules_meta.yml.j2 +++ b/templates/galaxy/config/tpv_rules_meta.yml.j2 @@ -160,7 +160,7 @@ destinations: # Ensuring a consistent collation environment is good for reproducibility. LC_ALL: C # The cache directory holds the docker containers that get converted - SINGULARITY_CACHEDIR: "/cvmfs/singularity.galaxyproject.org/all/" + SINGULARITY_CACHEDIR: "{{ galaxy_mutable_data_dir }}/singularity/cache" # Singularity uses a temporary directory to build the squashfs filesystem SINGULARITY_TMPDIR: "{{ galaxy_mutable_data_dir }}/tmp" scheduling: @@ -202,7 +202,8 @@ destinations: TMPDIR: $SCRATCHDIR TMP: $SCRATCHDIR TEMP: $SCRATCHDIR - SINGULARITY_CACHEDIR: "/cvmfs/singularity.galaxyproject.org/all/" + APPTAINER_CACHEDIR: "/storage/{{ pulsar.nfs_home }}/home/{{ pulsar.user_name }}/.singularity/cache/" + SINGULARITY_CACHEDIR: "/storage/{{ pulsar.nfs_home }}/home/{{ pulsar.user_name }}/.singularity/cache/" SINGULARITY_TMPDIR: $SCRATCHDIR XDG_CACHE_HOME: $SCRATCHDIR scheduling: From 5ebbaa121a197911398faedb6f3e38794f5a5ed7 Mon Sep 17 00:00:00 2001 From: Martin Demko <325073@mail.muni.cz> Date: Thu, 17 Apr 2025 12:46:49 +0200 Subject: [PATCH 2/2] adds cached_explicit_singularity --- group_vars/galaxyservers.yml | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/group_vars/galaxyservers.yml b/group_vars/galaxyservers.yml index e880cdc..9464a14 100644 --- a/group_vars/galaxyservers.yml +++ b/group_vars/galaxyservers.yml @@ -153,14 +153,15 @@ galaxy_config: - /cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml # Tool Dependencies container_resolvers: + - type: cached_explicit_singularity + cache_directory: "/storage/{{ pulsar.nfs_home }}/home/{{ pulsar.user_name }}/.singularity/cache/" - type: explicit_singularity - - cache_directory: /cvmfs/singularity.galaxyproject.org/all/ - type: cached_mulled_singularity - - auto_install: true - type: mulled_singularity - - auto_install: false - type: build_mulled_singularity -# cache_directory: /cvmfs/singularity.galaxyproject.org/all/ + - type: cached_mulled_singularity + cache_directory: /cvmfs/singularity.galaxyproject.org/all/ + - type: mulled_singularity + auto_install: true + - type: build_mulled_singularity + auto_install: false cache_directory: "{{ galaxy_mutable_data_dir }}/singularity/mulled" # Data Library Directories library_import_dir: "{{ csnt_library_import_dir }}"