diff --git a/group_vars/gxconfig.yml b/group_vars/gxconfig.yml index 4b1a864cc..897a70030 100644 --- a/group_vars/gxconfig.yml +++ b/group_vars/gxconfig.yml @@ -373,7 +373,7 @@ base_app_main: &BASE_APP_MAIN # If this is set to None, the default container resolvers loaded is # determined by enable_mulled_containers. For available options see # https://docs.galaxyproject.org/en/master/admin/container_resolvers.html - container_resolvers_config_file: "{{ galaxy_config_dir }}/container_resolvers_conf.xml" + container_resolvers_config_file: "{{ galaxy_config_dir }}/container_resolvers_conf.yml" # Rather than specifying a container_resolvers_config_file, the # definition of the resolvers to enable can be embedded into Galaxy's diff --git a/group_vars/sn06.yml b/group_vars/sn06.yml index 57fd2068a..f8570d7c0 100644 --- a/group_vars/sn06.yml +++ b/group_vars/sn06.yml @@ -415,7 +415,7 @@ galaxy_config_templates: dest: "{{ galaxy_server_dir }}/lib/galaxy/tools/toolbox/filters/global_host_filters.py" - src: "{{ galaxy_config_template_src_dir }}/config/job_conf.yml.j2" dest: "{{ galaxy_config_dir }}/job_conf.yml" - - src: "{{ galaxy_config_template_src_dir }}/config/container_resolvers_conf.xml.j2" + - src: "{{ galaxy_config_template_src_dir }}/config/container_resolvers_conf.yml.j2" dest: "{{ galaxy_config_dir }}/container_resolvers_conf.xml" - src: "{{ galaxy_config_template_src_dir }}/config/user_filters.py.j2" dest: "{{ galaxy_server_dir }}/lib/galaxy/tools/toolbox/filters/user_filters.py" diff --git a/group_vars/sn07.yml b/group_vars/sn07.yml index 5a3e8bf8e..93a9e63d9 100644 --- a/group_vars/sn07.yml +++ b/group_vars/sn07.yml @@ -451,7 +451,7 @@ galaxy_config_templates: dest: "{{ galaxy_server_dir }}/lib/galaxy/tool_util/toolbox/filters/global_host_filters.py" - src: "{{ galaxy_config_template_src_dir }}/config/job_conf.yml.j2" dest: "{{ galaxy_config_dir }}/job_conf.yml" - - src: "{{ galaxy_config_template_src_dir }}/config/container_resolvers_conf.xml.j2" + - src: "{{ galaxy_config_template_src_dir }}/config/container_resolvers_conf.yml.j2" dest: "{{ galaxy_config_dir }}/container_resolvers_conf.xml" - src: "{{ galaxy_config_template_src_dir }}/config/user_filters.py.j2" dest: "{{ galaxy_server_dir }}/lib/galaxy/tool_util/toolbox/filters/user_filters.py" diff --git a/templates/galaxy/config/container_resolvers_conf.xml.j2 b/templates/galaxy/config/container_resolvers_conf.xml.j2 deleted file mode 100644 index 934028d33..000000000 --- a/templates/galaxy/config/container_resolvers_conf.xml.j2 +++ /dev/null @@ -1,64 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/templates/galaxy/config/container_resolvers_conf.yml.j2 b/templates/galaxy/config/container_resolvers_conf.yml.j2 new file mode 100644 index 000000000..c3386661a --- /dev/null +++ b/templates/galaxy/config/container_resolvers_conf.yml.j2 @@ -0,0 +1,128 @@ +# Sample file for container resolvers. Resolvers that are potentially used by default +# are uncommented (comments describe under which premises they are in the +# defaults). + +# Note that commented yaml does not have a space after the # +# while additional explanations do. + +# Explicit container resolvers +# ============================ + +# get a container description (URI) for an explicit docker container requirement +- type: explicit + +# get a container description (URI) for an explicit singularity container requirement +- type: explicit_singularity + +# get a cached container description (path) for singularity +# pulls the container into a cache directory if not yet there +#- type: cached_explicit_singularity + # set the cache directory for storing images + #cache_directory: database/container_cache/singularity/explicit + +# Mulled container resolvers +# ========================== + +# The following uncommented container resolvers are in the defaults +# if ``enable_mulled_containers`` is set in ``galaxy.yml`` (which is the default). + +# get a container description to a cached mulled docker container +- type: cached_mulled + # This resolver type will check the image cache for `quay.io/NAMESPACE/containername` + # The image cache can be populated by `mulled_*` resolvers or + # with a manual `docker pull quay.io/NAMESPACE/containername`. + namespace: biocontainers +#- type: cached_mulled +# namespace: local +# # The local namespace refers to locally built images that are prefixed with quay.io/local/. +# #namespace: biocontainers +# # the version of the mulled hashing function (v2/v1) +# #hash_func: v2 + + + +# checks if the image file exists in `cache_directory` +- type: cached_mulled_singularity + #namespace: biocontainers + cache_directory: "/cvmfs/singularity.galaxyproject.org/all/" + # + # the method for caching directory listings (not the method for image caching) + # can be uncached or dir_mtime (the latter only determines the directory listing + # if the modification time of the directory changed) + #cache_directory_cacher_type: uncached + +#- type: cached_mulled_singularity +# namespace: local +# #cache_directory_cacher_type: uncached + +# Resolves container images from quay.io/NAMESPACE/MULLED_HASH where the +# mulled hash describes which packages and versions should be in the container +# +# If the docker CLI is available the image will be pulled. +# +# These resolvers are generally listed after the cached_* resolvers, so that images +# are not pulled if they are already cached. +- type: mulled + namespace: biocontainers + # + # If true return quay.io/NAMESPACE/MULLED_HASH otherwise to the cached image + # which is also quay.io/NAMESPACE/MULLED_HASH in case of docker + #auto_install: true + +# Differences with the docker `mulled` resolver are +# - when pulling the image file will be stored in the configured cache dir +# - if auto_install is True the result will point to the cached image file +# and to quay.io/NAMESPACE/MULLED_HASH otherwise +- type: mulled_singularity + namespace: biocontainers + # In addition to the arguments of `mulled` there are cache_directory + # and cache_directory_cacher_type. See the description at `cached_explicit_singularity` + # and note the minor difference in the default for `cache_directory` + cache_directory: "/cvmfs/singularity.galaxyproject.org/all/" + #cache_directory_cacher_type: uncached + +# Building container resolvers +# ---------------------------- +# +# The following uncommented container resolvers are included in the default +# if ``docker`` is available + +#- type: build_mulled +# #namespace: local +# #hash_func: v2 +# #auto_install: true +#- type: build_mulled_singularity +# #hash_func: v2 +# #auto_install: true +# #cache_directory: database/container_cache/singularity/mulled +# #cache_directory_cacher_type: uncached + + +# Other explicit container resolvers +# ---------------------------------- + +#- type: fallback + #identifier: A_VALID_CONTAINER_IDENTIFIER + +- type: fallback_singularity + identifier: "/data/0/singularity_base_images/centos:8.3.2011" +#- type: fallback_no_requirements + #identifier: A_VALID_CONTAINER_IDENTIFIER +- type: fallback_no_requirements_singularity + identifier: "/data/0/singularity_base_images/centos:8.3.2011" +#- type: requires_galaxy_environment + #identifier: A_VALID_CONTAINER_IDENTIFIER +#- type: requires_galaxy_environment_singularity + #identifier: A_VALID_CONTAINER_IDENTIFIER + +# The mapping container resolver allows to specify a list of mappings from tools +# (tool_id) to containers (type and identifier). + +#-type: mapping + #mappings: + #- container_type: docker + #tool_id: A_TOOL_ID + #identifier: A_VALID_CONTAINER_IDENTIFIER + #- container_type: singularity + #tool_id: A_TOOL_ID + #identifier: A_VALID_CONTAINER_IDENTIFIER# get a container description for a cached mulled singularity container