Snakemake storage plugin: ftp

This plugin allows to transparently handle input and output files on any FTP server, including FTPS. For sFTP (FTP over SSH), use the sftp plugin instead.

Installation

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

pip install snakemake-storage-plugin-ftp

Usage

Queries

Queries to this storage should have the following format:

Query type	Query	Description
any	ftp://ftpserver.com:21/myfile.txt	A file on an ftp server. The port is optional and defaults to 21.
any	ftps://ftpserver.com:21/myfile.txt	A file on an ftp server (using encrypted transport). The port is optional and defaults to 21.

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 ftp --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 ftp --default-storage-prefix ... \
    --storage-ftp-max-requests-per-second ... \        --storage-ftp-username ... \        --storage-ftp-password ... \        --storage-ftp-active-mode ...

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="ftp",
    # optionally add custom settings here if needed
    # alternatively they can be passed via command line arguments
    # starting with --storage-ftp-..., 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=...,
    # FTP username
    username=...,
    # FTP password
    password=...,
    # Use active mode instead of passive mode
    active_mode=...,

rule example:
    input:
        storage.ftp(
            # 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="ftp",
    # optionally add custom settings here if needed
    # alternatively they can be passed via command line arguments
    # starting with --storage-ftp-..., 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=...,
    # FTP username
    username=...,
    # FTP password
    password=...,
    # Use active mode instead of passive mode
    active_mode=...,

# register multiple tagged entities
storage foo:
    provider="ftp",
    # optionally add custom settings here if needed
    # alternatively they can be passed via command line arguments
    # starting with --storage-ftp-..., 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=...,
    # FTP username
    username=...,
    # FTP password
    password=...,
    # Use active mode instead of passive mode
    active_mode=...,

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-ftp-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-ftp-username VALUE	username	SNAKEMAKE_STORAGE_FTP_USERNAME	FTP username	None		✗	str
--storage-ftp-password VALUE	password	SNAKEMAKE_STORAGE_FTP_PASSWORD	FTP password	None		✗	str
--storage-ftp-active-mode VALUE	active_mode	SNAKEMAKE_STORAGE_FTP_ACTIVE_MODE	Use active mode instead of passive mode	False		✗	str