Snakemake storage plugin: irods
Warning
No documentation found in repository https://github.com/snakemake/snakemake-storage-plugin-irods. 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 instructions presented in this catalog.
Installation
Install this plugin by installing it with pip or mamba, e.g.:
pip install snakemake-storage-plugin-irods
Usage
Queries
Queries to this storage should have the following format:
Query type |
Query |
Description |
|---|---|---|
any |
|
A file in a folder on the iRODS server. |
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 irods --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 irods --default-storage-prefix ... \
--storage-irods-max-requests-per-second ... \ --storage-irods-host ... \ --storage-irods-port ... \ --storage-irods-username ... \ --storage-irods-password ... \ --storage-irods-zone ... \ --storage-irods-home ... \ --storage-irods-authentication-scheme ... \ --storage-irods-encryption-algorithm ... \ --storage-irods-encryption-key-size ... \ --storage-irods-encryption-num-hash-rounds ... \ --storage-irods-encryption-salt-size ... \ --storage-irods-client-server-negotiation ... \ --storage-irods-client-server-policy ... \ --storage-irods-ssl-verify-server ... \ --storage-irods-ssl-ca-certificate-file ... \ --storage-irods-use-ssl ...
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="irods",
# optionally add custom settings here if needed
# alternatively they can be passed via command line arguments
# starting with --storage-irods-..., 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 host name of the iRODS server. Value in ~/.irods/irods_environment.json has higher priority, if present.
host=...,
# The port of the iRODS server. Value in ~/.irods/irods_environment.json has higher priority, if present.
port=...,
# The user name for the iRODS server. Value in ~/.irods/irods_environment.json has higher priority, if present.
username=...,
# The password for the iRODS server. Value in ~/.irods/irods_environment.json has higher priority, if present. If no password is provided in the settings or environment file, the password in ~/.irods/.irodsA will be used with native authentication.
password=...,
# The zone for the iRODS server. Value in ~/.irods/irods_environment.json has higher priority, if present.
zone=...,
# The home parameter for the iRODS server. Value in ~/.irods/irods_environment.json has higher priority, if present.
home=...,
# The authentication scheme for the iRODS server. Value in ~/.irods/irods_environment.json has higher priority, if present. If no password is provided in the settings or environment file, the password in ~/.irods/.irodsA will be used with native authentication.
authentication_scheme=...,
# Encryption algorithm for parallel transfer encryption. Value in ~/.irods/irods_environment.json has higher priority, if present.
encryption_algorithm=...,
# Key size for parallel transfer encryption. Value in ~/.irods/irods_environment.json has higher priority, if present.
encryption_key_size=...,
# Number of hash rounds for parallel transfer encryption. Value in ~/.irods/irods_environment.json has higher priority, if present.
encryption_num_hash_rounds=...,
# Salt size for parallel transfer encryption. Value in ~/.irods/irods_environment.json has higher priority, if present.
encryption_salt_size=...,
# Set to 'request_server_negotiation' to enable SSL/TLS. Value in ~/.irods/irods_environment.json has higher priority, if present.
client_server_negotiation=...,
# CS_NEG_REFUSE: no SSL/TLS, CS_NEG_REQUIRE: enforce SSL/TLS, CS_NEG_DONT_CARE: let server decide. Value in ~/.irods/irods_environment.json has higher priority, if present.
client_server_policy=...,
# none: do not verify certificate, cert: verify certificate validity (but not hostname), hostname: verify certificate validity and hostname. Value in ~/.irods/irods_environment.json has higher priority, if present.
ssl_verify_server=...,
# Path to file with trusted CA certificates in PEM format. Used in conjunction with system default trusted certificates. Value in ~/.irods/irods_environment.json has higher priority, if present.
ssl_ca_certificate_file=...,
# Whether to use SSL when connecting to the server.
use_ssl=...,
rule example:
input:
storage.irods(
# 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="irods",
# optionally add custom settings here if needed
# alternatively they can be passed via command line arguments
# starting with --storage-irods-..., 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 host name of the iRODS server. Value in ~/.irods/irods_environment.json has higher priority, if present.
host=...,
# The port of the iRODS server. Value in ~/.irods/irods_environment.json has higher priority, if present.
port=...,
# The user name for the iRODS server. Value in ~/.irods/irods_environment.json has higher priority, if present.
username=...,
# The password for the iRODS server. Value in ~/.irods/irods_environment.json has higher priority, if present. If no password is provided in the settings or environment file, the password in ~/.irods/.irodsA will be used with native authentication.
password=...,
# The zone for the iRODS server. Value in ~/.irods/irods_environment.json has higher priority, if present.
zone=...,
# The home parameter for the iRODS server. Value in ~/.irods/irods_environment.json has higher priority, if present.
home=...,
# The authentication scheme for the iRODS server. Value in ~/.irods/irods_environment.json has higher priority, if present. If no password is provided in the settings or environment file, the password in ~/.irods/.irodsA will be used with native authentication.
authentication_scheme=...,
# Encryption algorithm for parallel transfer encryption. Value in ~/.irods/irods_environment.json has higher priority, if present.
encryption_algorithm=...,
# Key size for parallel transfer encryption. Value in ~/.irods/irods_environment.json has higher priority, if present.
encryption_key_size=...,
# Number of hash rounds for parallel transfer encryption. Value in ~/.irods/irods_environment.json has higher priority, if present.
encryption_num_hash_rounds=...,
# Salt size for parallel transfer encryption. Value in ~/.irods/irods_environment.json has higher priority, if present.
encryption_salt_size=...,
# Set to 'request_server_negotiation' to enable SSL/TLS. Value in ~/.irods/irods_environment.json has higher priority, if present.
client_server_negotiation=...,
# CS_NEG_REFUSE: no SSL/TLS, CS_NEG_REQUIRE: enforce SSL/TLS, CS_NEG_DONT_CARE: let server decide. Value in ~/.irods/irods_environment.json has higher priority, if present.
client_server_policy=...,
# none: do not verify certificate, cert: verify certificate validity (but not hostname), hostname: verify certificate validity and hostname. Value in ~/.irods/irods_environment.json has higher priority, if present.
ssl_verify_server=...,
# Path to file with trusted CA certificates in PEM format. Used in conjunction with system default trusted certificates. Value in ~/.irods/irods_environment.json has higher priority, if present.
ssl_ca_certificate_file=...,
# Whether to use SSL when connecting to the server.
use_ssl=...,
# register multiple tagged entities
storage foo:
provider="irods",
# optionally add custom settings here if needed
# alternatively they can be passed via command line arguments
# starting with --storage-irods-..., 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 host name of the iRODS server. Value in ~/.irods/irods_environment.json has higher priority, if present.
host=...,
# The port of the iRODS server. Value in ~/.irods/irods_environment.json has higher priority, if present.
port=...,
# The user name for the iRODS server. Value in ~/.irods/irods_environment.json has higher priority, if present.
username=...,
# The password for the iRODS server. Value in ~/.irods/irods_environment.json has higher priority, if present. If no password is provided in the settings or environment file, the password in ~/.irods/.irodsA will be used with native authentication.
password=...,
# The zone for the iRODS server. Value in ~/.irods/irods_environment.json has higher priority, if present.
zone=...,
# The home parameter for the iRODS server. Value in ~/.irods/irods_environment.json has higher priority, if present.
home=...,
# The authentication scheme for the iRODS server. Value in ~/.irods/irods_environment.json has higher priority, if present. If no password is provided in the settings or environment file, the password in ~/.irods/.irodsA will be used with native authentication.
authentication_scheme=...,
# Encryption algorithm for parallel transfer encryption. Value in ~/.irods/irods_environment.json has higher priority, if present.
encryption_algorithm=...,
# Key size for parallel transfer encryption. Value in ~/.irods/irods_environment.json has higher priority, if present.
encryption_key_size=...,
# Number of hash rounds for parallel transfer encryption. Value in ~/.irods/irods_environment.json has higher priority, if present.
encryption_num_hash_rounds=...,
# Salt size for parallel transfer encryption. Value in ~/.irods/irods_environment.json has higher priority, if present.
encryption_salt_size=...,
# Set to 'request_server_negotiation' to enable SSL/TLS. Value in ~/.irods/irods_environment.json has higher priority, if present.
client_server_negotiation=...,
# CS_NEG_REFUSE: no SSL/TLS, CS_NEG_REQUIRE: enforce SSL/TLS, CS_NEG_DONT_CARE: let server decide. Value in ~/.irods/irods_environment.json has higher priority, if present.
client_server_policy=...,
# none: do not verify certificate, cert: verify certificate validity (but not hostname), hostname: verify certificate validity and hostname. Value in ~/.irods/irods_environment.json has higher priority, if present.
ssl_verify_server=...,
# Path to file with trusted CA certificates in PEM format. Used in conjunction with system default trusted certificates. Value in ~/.irods/irods_environment.json has higher priority, if present.
ssl_ca_certificate_file=...,
# Whether to use SSL when connecting to the server.
use_ssl=...,
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):