SnakeDeploy

Deploy a snakemake pipeline from GitHub.

Getting Started

SnakeDeploy is the start of a command line and interactive Python client to easily deploy snakemake pipelines from version control like GitHub.

1. Install

You first might want to install the software. You can do this from GitHub or from pypi.

pip install snakedeploy

or

git clone git@github.com:snakemake/snakedeploy.git
cd snakedeploy
pip install .

If you plan to develop and want to install from the local folder, you can do:

pip install -e .

You can then interact with the client.

$ snakedeploy --help
usage: snakedeploy [-h] [--version] [--verbose] [--log-disable-color] [--log-use-threads] [--force] repo dest {version} ...

Snakedeploy: deploy snakemake pipelines from version control.

positional arguments:
  repo                 Repository address and destination to deploy, e.g., <source> <dest>
  dest                 Path to clone the repository, should not exist.

optional arguments:
  -h, --help           show this help message and exit
  --version            suppress additional output.
  --verbose            verbose output for logging.
  --log-disable-color  Disable color for snakedeploy logging.
  --log-use-threads    Force threads rather than processes.
  --force              If the folder exists, force overwrite, meaning remove and replace.

actions:
  snakedeploy subparsers

  {version}            snakedeploy actions
    version            show software version

2. Deploy

Command Line

The simplest functionality is to deploy a pipeline, which basically means cloning a repository to a particular destination. You can do that as follows:

$ snakedeploy https://github.com/snakemake-workflows/dna-seq-varlociraptor /tmp/dest

You'll then see the repository clone

Cloning into '/tmp/dest'...
remote: Enumerating objects: 99, done.
remote: Counting objects: 100% (99/99), done.
remote: Compressing objects: 100% (71/71), done.
remote: Total 1762 (delta 52), reused 55 (delta 26), pack-reused 1663
Receiving objects: 100% (1762/1762), 19.44 MiB | 2.63 MiB/s, done.
Resolving deltas: 100% (1122/1122), done.
Repository snakemake-workflows/dna-seq-varlociraptor cloned to /tmp/dest. Edit config and sample sheets.

And inspect the files there!

$ ls /tmp/dest/
config  LICENSE  README.md  workflow

Python

These same interactions can be done from within Python.

from snakedeploy.providers import ProviderRunner
provider = ProviderRunner()
dest = provider.deploy("https://github.com/snakemake-workflows/dna-seq-varlociraptor", "/tmp/dest")

The library is fairly simple now, but will be used as a base for an interactive tool to run snakemake workflows. Stay tuned!

License

• Free software: MPL 2.0 License