Snakemake storage plugin: xrootd

Warning

No documentation found in repository https://github.com/snakemake/snakemake-storage-plugin-xrootd. The plugin should provide a docs/intro.md with some introductory sentences and optionally a docs/further.md file with details beyond the auto-generated usage instractions presented in this catalog.

Installation

Install this plugin by installing it with pip or mamba, e.g.:

pip install snakemake-storage-plugin-xrootd

Usage

Queries

Queries to this storage should have the following format:

Query type	Query	Description
any	root://eos/user/s/someuser/somefile.txt	A file on an XrootD instance. Note that we omit the host name from the query as that is given via the settings of the storage provider.

As default provider

If you want all your input and output (which is not explicitly marked to come from another storage) to be written to and read from this storage, you can use it as a default provider via:

snakemake --default-storage-provider xrootd --default-storage-prefix ...

with ... being the prefix of a query under which you want to store all your results. You can also pass custom settings via command line arguments:

snakemake --default-storage-provider xrootd --default-storage-prefix ... \
    --storage-xrootd-max-requests-per-second ... \        --storage-xrootd-host ... \        --storage-xrootd-port ... \        --storage-xrootd-username ... \        --storage-xrootd-password ... \        --storage-xrootd-query-params ...

Within the workflow

If you want to use this storage plugin only for specific items, you can register it inside of your workflow:

# register storage provider (not needed if no custom settings are to be defined here)
storage:
    provider="xrootd",
    # optionally add custom settings here if needed
    # alternatively they can be passed via command line arguments
    # starting with --storage-xrootd-..., see
    # snakemake --help
    # Maximum number of requests per second for this storage provider. If nothing is specified, the default implemented by the storage plugin is used.
    max_requests_per_second=...,
    # The XrootD host to connect to
    host=...,
    # The XrootD port to connect to
    port=...,
    # The username to use for authentication
    username=...,
    # The password to use for authentication
    password=...,
    # Optional query parameters for XRootD (e.g. xrd.wantprot=unix, authz=XXXXXX)
    query_params=...,

rule example:
    input:
        storage.xrootd(
            # define query to the storage backend here
            ...
        ),
    output:
        "example.txt"
    shell:
        "..."

Using multiple entities of the same storage plugin

In case you have to use this storage plugin multiple times, but with different settings (e.g. to connect to different storage servers), you can register it multiple times, each time providing a different tag:

# register shared settings
storage:
    provider="xrootd",
    # optionally add custom settings here if needed
    # alternatively they can be passed via command line arguments
    # starting with --storage-xrootd-..., see below
    # Maximum number of requests per second for this storage provider. If nothing is specified, the default implemented by the storage plugin is used.
    max_requests_per_second=...,
    # The XrootD host to connect to
    host=...,
    # The XrootD port to connect to
    port=...,
    # The username to use for authentication
    username=...,
    # The password to use for authentication
    password=...,
    # Optional query parameters for XRootD (e.g. xrd.wantprot=unix, authz=XXXXXX)
    query_params=...,

# register multiple tagged entities
storage foo:
    provider="xrootd",
    # optionally add custom settings here if needed
    # alternatively they can be passed via command line arguments
    # starting with --storage-xrootd-..., see below.
    # To only pass a setting to this tagged entity, prefix the given value with
    # the tag name, i.e. foo:max_requests_per_second=...
    # Maximum number of requests per second for this storage provider. If nothing is specified, the default implemented by the storage plugin is used.
    max_requests_per_second=...,
    # The XrootD host to connect to
    host=...,
    # The XrootD port to connect to
    port=...,
    # The username to use for authentication
    username=...,
    # The password to use for authentication
    password=...,
    # Optional query parameters for XRootD (e.g. xrd.wantprot=unix, authz=XXXXXX)
    query_params=...,

rule example:
    input:
        storage.foo(
            # define query to the storage backend here
            ...
        ),
    output:
        "example.txt"
    shell:
        "..."

Settings

The storage plugin has the following settings (which can be passed via command line, the workflow or environment variables, if provided in the respective columns):

CLI setting	Workflow setting	Envvar setting	Description	Default	Choices	Required	Type
--storage-xrootd-max-requests-per-second VALUE	max_requests_per_second		Maximum number of requests per second for this storage provider. If nothing is specified, the default implemented by the storage plugin is used.	None		✗	str
--storage-xrootd-host VALUE	host		The XrootD host to connect to	None		✓	str
--storage-xrootd-port VALUE	port		The XrootD port to connect to	None		✗	str
--storage-xrootd-username VALUE	username	SNAKEMAKE_STORAGE_XROOTD_USERNAME	The username to use for authentication	None		✗	str
--storage-xrootd-password VALUE	password	SNAKEMAKE_STORAGE_XROOTD_PASSWORD	The password to use for authentication	None		✗	str
--storage-xrootd-query-params VALUE	query_params	SNAKEMAKE_STORAGE_XROOTD_QUERY_PARAMS	Optional query parameters for XRootD (e.g. xrd.wantprot=unix, authz=XXXXXX)	None		✗	str