-
Notifications
You must be signed in to change notification settings - Fork 96
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Container to container resolver XML file to YAML #868
base: master
Are you sure you want to change the base?
Changes from all commits
File filter
Filter by extension
Conversations
Jump to
Diff view
Diff view
There are no files selected for viewing
Original file line number | Diff line number | Diff line change | ||||
---|---|---|---|---|---|---|
|
@@ -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" | ||||||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more.
Suggested change
|
||||||
- src: "{{ galaxy_config_template_src_dir }}/config/user_filters.py.j2" | ||||||
dest: "{{ galaxy_server_dir }}/lib/galaxy/tool_util/toolbox/filters/user_filters.py" | ||||||
|
This file was deleted.
Original file line number | Diff line number | Diff line change | ||||||
---|---|---|---|---|---|---|---|---|
@@ -0,0 +1,128 @@ | ||||||||
# Sample file for container resolvers. Resolvers that are potentially used by default | ||||||||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more.
Suggested change
Just because the file is used in production now. |
||||||||
# 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/" | ||||||||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more.
Suggested change
|
||||||||
# | ||||||||
# 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 | ||||||||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more.
Suggested change
We have auto install explicitly set to |
||||||||
|
||||||||
# 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 | ||||||||
|
||||||||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more.
Suggested change
Same story as before, we have |
||||||||
# 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 |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.