Remote files

In versions snakemake>=3.5.

The Snakefile supports a wrapper function, remote(), indicating a file is on a remote storage provider (this is similar to temp() or protected()). In order to use all types of remote files, the Python packages boto, moto, filechunkio, pysftp, dropbox, requests, and ftputil must be installed.

During rule execution, a remote file (or object) specified is downloaded to the local cwd, within a sub-directory bearing the same name as the remote provider. This sub-directory naming lets you have multiple remote origins with reduced likelihood of name collisions, and allows Snakemake to easily translate remote objects to local file paths. You can think of each local remote sub-directory as a local mirror of the remote system. The remote() wrapper is mutually-exclusive with the temp() and protected() wrappers.

Snakemake includes the following remote providers, supported by the corresponding classes:

  • Amazon Simple Storage Service (AWS S3): snakemake.remote.S3
  • Google Cloud Storage (GS): snakemake.remote.GS
  • File transfer over SSH (SFTP): snakemake.remote.SFTP
  • Read-only web (HTTP[S]): snakemake.remote.HTTP
  • File transfer protocol (FTP): snakemake.remote.FTP
  • Dropbox: snakemake.remote.dropbox

Amazon Simple Storage Service (S3)

This section describes usage of the S3 RemoteProvider, and also provides an intro to remote files and their usage.

It is important to note that you must have credentials (access_key_id and secret_access_key) which permit read/write access. If a file only serves as input to a Snakemake rule, read access is sufficient. You may specify credentials as environment variables or in the file =/.aws/credentials, prefixed with AWS_*, as with a standard boto config. Credentials may also be explicitly listed in the Snakefile, as shown below:

For the Amazon S3 and Google Cloud Storage providers, the sub-directory used must be the bucket name.

Using remote files is easy (AWS S3 shown):

from snakemake.remote.S3 import RemoteProvider as S3RemoteProvider
S3 = S3RemoteProvider(access_key_id="MYACCESSKEY", secret_access_key="MYSECRET")

rule all:
    input:
        S3.remote("bucket-name/file.txt")

Expand still works as expected, just wrap the expansion:

from snakemake.remote.S3 import RemoteProvider as S3RemoteProvider
S3 = S3RemoteProvider()

rule all:
    input:
        S3.remote(expand("bucket-name/{letter}-2.txt", letter=["A", "B", "C"]))

It is possible to use S3-compatible storage by specifying a different endpoint address as the host kwarg in the provider, as the kwargs used in instantiating the provider are passed in to boto:

from snakemake.remote.S3 import RemoteProvider as S3RemoteProvider
S3 = S3RemoteProvider(access_key_id="MYACCESSKEY", secret_access_key="MYSECRET", host="mystorage.example.com")

rule all:
    input:
        S3.remote("bucket-name/file.txt")

Only remote files needed to satisfy the DAG build are downloaded for the workflow. By default, remote files are downloaded prior to rule execution and are removed locally as soon as no rules depend on them. Remote files can be explicitly kept by setting the keep_local=True keyword argument:

from snakemake.remote.S3 import RemoteProvider as S3RemoteProvider
S3 = S3RemoteProvider(access_key_id="MYACCESSKEY", secret_access_key="MYSECRET")

rule all:
    input: S3.remote('bucket-name/prefix{split_id}.txt', keep_local=True)

If you wish to have a rule to simply download a file to a local copy, you can do so by declaring the same file path locally as is used by the remote file:

from snakemake.remote.S3 import RemoteProvider as S3RemoteProvider
S3 = S3RemoteProvider(access_key_id="MYACCESSKEY", secret_access_key="MYSECRET")

rule all:
    input:
        S3.remote("bucket-name/out.txt")
    output:
        "bucket-name/out.txt"
    run:
        shell("cp {output[0]} ./")

The remote provider also supports a new glob_wildcards() (see How do I run my rule on all files of a certain directory?) which acts the same as the local version of glob_wildcards(), but for remote files:

from snakemake.remote.S3 import RemoteProvider as S3RemoteProvider
S3 = S3RemoteProvider(access_key_id="MYACCESSKEY", secret_access_key="MYSECRET")
S3.glob_wildcards("bucket-name/{file_prefix}.txt")

# (result looks just like as if the local glob_wildcards() function were used on a locally with a folder called "bucket-name")

Google Cloud Storage (GS)

Using Google Cloud Storage (GS) is a simple import change, though since GS support it is based on boto, GS must be accessed via Google’s “interoperable” credentials. Usage of the GS provider is the same as the S3 provider. You may specify credentials as environment variables in the file =/.aws/credentials, prefixed with AWS_*, as with a standard boto config, or explicitly in the Snakefile.

from snakemake.remote.GS import RemoteProvider as GSRemoteProvider
GS = GSRemoteProvider(access_key_id="MYACCESSKEY", secret_access_key="MYSECRET")

rule all:
    input:
        GS.remote("bucket-name/file.txt")

File transfer over SSH (SFTP)

Snakemake can use files on remove servers accessible via SFTP (i.e. most *nix servers). It uses pysftp for the underlying support of SFTP, so the same connection options exist. Assuming you have SSH keys already set up for the server you are using in the Snakefile, usage is simple:

from snakemake.remote.SFTP import RemoteProvider
SFTP = RemoteProvider()

rule all:
    input:
        SFTP.remote("example.com/path/to/file.bam")

The remote file addresses used must be specified with the host (domain or IP address) and the absolute path to the file on the remote server. A port may be specified if the SSH daemon on the server is listening on a port other than 22, in either the RemoteProvider or in each instance of remote():

from snakemake.remote.SFTP import RemoteProvider
SFTP = RemoteProvider(port=4040)

rule all:
    input:
        SFTP.remote("example.com/path/to/file.bam")
from snakemake.remote.SFTP import RemoteProvider
SFTP = RemoteProvider()

rule all:
    input:
        SFTP.remote("example.com:4040/path/to/file.bam")

The standard keyword arguments used by pysftp may be provided to the RemoteProvider to specify credentials (either password or private key):

from snakemake.remote.SFTP import RemoteProvider
SFTP = RemoteProvider(username="myusername", private_key="/Users/myusername/.ssh/particular_id_rsa")

rule all:
    input:
        SFTP.remote("example.com/path/to/file.bam")
from snakemake.remote.SFTP import RemoteProvider
SFTP = RemoteProvider(username="myusername", password="mypassword")

rule all:
    input:
        SFTP.remote("example.com/path/to/file.bam")

If you share credentials between servers but connect to one on a different port, the alternate port may be specified in the remote() wrapper:

from snakemake.remote.SFTP import RemoteProvider
SFTP = RemoteProvider(username="myusername", password="mypassword")

rule all:
    input:
        SFTP.remote("some-example-server-1.com/path/to/file.bam"),
        SFTP.remote("some-example-server-2.com:2222/path/to/file.bam")

There is a glob_wildcards() function:

from snakemake.remote.SFTP import RemoteProvider
SFTP = RemoteProvider()
SFTP.glob_wildcards("example.com/path/to/{sample}.bam")

Read-only web (HTTP[s])

Snakemake can access web resources via a read-only HTTP(S) provider. This provider can be helpful for including public web data in a workflow.

Web addresses must be specified without protocol, so if your URI looks like this:

http://server3.example.com/path/to/myfile.tar.gz

The URI used in the Snakefile must look like this:

server3.example.com/path/to/myfile.tar.gz

It is straightforward to use the HTTP provider to download a file to the cwd:

import os
from snakemake.remote.HTTP import RemoteProvider as HTTPRemoteProvider

HTTP = HTTPRemoteProvider()

rule all:
    input:
        HTTP.remote("www.example.com/path/to/document.pdf", keep_local=True)
    run:
        outputName = os.path.basename(input[0])
        shell("mv {input} {outputName}")

To connect on a different port, specify the port as part of the URI string:

from snakemake.remote.HTTP import RemoteProvider as HTTPRemoteProvider
HTTP = HTTPRemoteProvider()

rule all:
    input:
        HTTP.remote("www.example.com:8080/path/to/document.pdf", keep_local=True)

By default, the HTTP provider always uses HTTPS (TLS). If you need to connect to a resource with regular HTTP (no TLS), you must explicitly include insecure as a kwarg to remote():

from snakemake.remote.HTTP import RemoteProvider as HTTPRemoteProvider
HTTP = HTTPRemoteProvider()

rule all:
    input:
        HTTP.remote("www.example.com/path/to/document.pdf", insecure=True, keep_local=True)

If the URI used includes characters not permitted in a local file path, you may include them as part of the additional_request_string in the kwargs for remote(). This may also be useful for including additional parameters you don not want to be part of the local filename (since the URI string becomes the local file name).

from snakemake.remote.HTTP import RemoteProvider as HTTPRemoteProvider
HTTP = HTTPRemoteProvider()

rule all:
    input:
        HTTP.remote("example.com/query.php", additional_request_string="?range=2;3")

If the file requires authentication, you can specify a username and password for HTTP Basic Auth with the Remote Provider, or with each instance of remote(). For different types of authentication, you can pass in a Python `requests.auth object (see here) the auth kwarg.

from snakemake.remote.HTTP import RemoteProvider as HTTPRemoteProvider
HTTP = HTTPRemoteProvider(username="myusername", password="mypassword")

rule all:
    input:
        HTTP.remote("example.com/interactive.php", keep_local=True)
from snakemake.remote.HTTP import RemoteProvider as HTTPRemoteProvider
HTTP = HTTPRemoteProvider()

rule all:
    input:
        HTTP.remote("example.com/interactive.php", username="myusername", password="mypassword", keep_local=True)
from snakemake.remote.HTTP import RemoteProvider as HTTPRemoteProvider
HTTP = HTTPRemoteProvider()

rule all:
    input:
        HTTP.remote("example.com/interactive.php", auth=requests.auth.HTTPDigestAuth("myusername", "mypassword"), keep_local=True)

Since remote servers do not present directory contents uniformly, glob_wildcards() is __not__ supported by the HTTP provider.

File Transfer Protocol (FTP)

Snakemake can work with files stored on regular FTP. Currently supported are authenticated FTP and anonymous FTP, excluding FTP via TLS.

Usage is similar to the SFTP provider, however the paths specified are relative to the FTP home directory (since this is typically a chroot):

from snakemake.remote.FTP import RemoteProvider as FTPRemoteProvider

FTP = FTPRemoteProvider(username="myusername", password="mypassword")

rule all:
    input:
        FTP.remote("example.com/rel/path/to/file.tar.gz")

The port may be specified in either the provider, or in each instance of remote():

from snakemake.remote.FTP import RemoteProvider as FTPRemoteProvider

FTP = FTPRemoteProvider(username="myusername", password="mypassword", port=2121)

rule all:
    input:
        FTP.remote("example.com/rel/path/to/file.tar.gz")
from snakemake.remote.FTP import RemoteProvider as FTPRemoteProvider

FTP = FTPRemoteProvider(username="myusername", password="mypassword")

rule all:
    input:
        FTP.remote("example.com:2121/rel/path/to/file.tar.gz")

Anonymous download of FTP resources is possible:

from snakemake.remote.FTP import RemoteProvider as FTPRemoteProvider
FTP = FTPRemoteProvider()

rule all:
    input:
        # only keeping the file so we can move it out to the cwd
        FTP.remote("example.com/rel/path/to/file.tar.gz", keep_local=True)
    run:
        shell("mv {input} ./")

glob_wildcards():

from snakemake.remote.FTP import RemoteProvider as FTPRemoteProvider
FTP = FTPRemoteProvider(username="myusername", password="mypassword")

print(FTP.glob_wildcards("example.com/somedir/{file}.txt"))

Dropbox

The Dropbox remote provider allows you to upload and download from your Dropbox account without having the client installed on your machine. In order to use the provider you first need to register an “app” on the Dropbox developer website, with access to the Full Dropbox. After registering, generate an OAuth2 access token. You will need the token to use the Snakemake Dropbox remote provider.

Using the Dropbox provider is straightforward:

from snakemake.remote.dropbox import RemoteProvider as DropboxRemoteProvider
DBox = DropboxRemoteProvider(oauth2_access_token="mytoken")

rule all:
    input:
        DBox.remote("path/to/input.txt")

glob_wildcards() is supported:

from snakemake.remote.dropbox import RemoteProvider as DropboxRemoteProvider
DBox = DropboxRemoteProvider(oauth2_access_token="mytoken")

DBox.glob_wildcards("path/to/{title}.txt")

Note that Dropbox paths are case-insensitive.

Remote cross-provider transfers

It is possible to use Snakemake to transfer files between remote providers (using the local machine as an intermediary), as long as the sub-directory (bucket) names differ:

from snakemake.remote.GS import RemoteProvider as GSRemoteProvider
from snakemake.remote.S3 import RemoteProvider as S3RemoteProvider

GS = GSRemoteProvider(access_key_id="MYACCESSKEYID", secret_access_key="MYSECRETACCESSKEY")
S3 = S3RemoteProvider(access_key_id="MYACCESSKEYID", secret_access_key="MYSECRETACCESSKEY")

fileList, = S3.glob_wildcards("source-bucket/{file}.bam")
rule all:
    input:
        GS.remote( expand("destination-bucket/{file}.bam", file=fileList) )
rule transfer_S3_to_GS:
    input:
        S3.remote( expand("source-bucket/{file}.bam", file=fileList) )
    output:
        GS.remote( expand("destination-bucket/{file}.bam", file=fileList) )
    run:
        shell("cp -R source-bucket/ destination-bucket/")