recipe toil

A scalable, efficient, cross-platform and easy-to-use workflow engine in pure Python

Homepage:

http://toil.ucsc-cgl.org/

Documentation:

https://toil.readthedocs.io/en/latest/

Developer docs:

https://github.com/DataBiosphere/toil

License:

Apache-2.0

Recipe:

/toil/meta.yaml

package toil

versions:

5.12.0-0,  5.11.0-0,  5.9.2-0,  5.7.1-0,  5.6.0-0,  5.5.0-1,  5.5.0-0,  5.4.0-0,  5.3.0-0, 

5.12.0-0,  5.11.0-0,  5.9.2-0,  5.7.1-0,  5.6.0-0,  5.5.0-1,  5.5.0-0,  5.4.0-0,  5.3.0-0,  5.2.0-0,  5.1.0-0,  5.0.0-0,  4.2.0-0,  4.1.0-0,  4.0.0-0,  3.24.0-0,  3.23.1-0,  3.21.0-0,  3.20.0-0,  3.14.0-2,  3.14.0-1,  3.14.0-0,  3.13.0a1-0,  3.11.0-1,  3.11.0-0,  3.11.0a1-1,  3.11.0a1-0,  3.10.0-0,  3.10.0a1-1,  3.10.0a1-0,  3.9.0a1-0,  3.8.0a1-1,  3.8.0a1-0,  3.7.0a-1,  3.7.0a-0,  3.6.0-0,  3.5.0a1-3,  3.5.0a1-2,  3.5.0a1-1,  3.5.0a1-0,  3.4.0a1-3,  3.4.0a1-2,  3.4.0a1-1,  3.4.0a1-0,  3.3.0a1-0,  3.2.0a2-2,  3.2.0a2-0

depends addict:

>=2.2.1

depends apache-libcloud:

>=2.2.1

depends cwltool:

3.1.20230601100705

depends dill:

>=0.3.2

depends docker-py:

>=3.7.2,<6

depends enlighten:

>=1.5.2

depends galaxy-tool-util:

depends google-cloud-storage:

>=2,<=2.8.0

depends idna:

>=2

depends mock:

>=4.0.3

depends networkx:

>=2,<2.8.9

depends psutil:

>=3.0.1

depends pynacl:

>=1.4.0

depends pypubsub:

>=4.0.3

depends python:

>=3.7

depends python-dateutil:

depends python-htcondor:

>=10.2.0.post1

depends python-kubernetes:

>=12.0.1,<22

depends pytz:

>=2012

depends requests:

>=2

depends ruamel.yaml:

>=0.15,<=0.17.21

depends ruamel.yaml.clib:

>=0.2.6

depends schema-salad:

>=8.4.20230128170514

depends typing-extensions:

depends urllib3:

>=1.26.0

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install toil

and update with::

   mamba update toil

To create a new environment, run:

mamba create --name myenvname toil

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/toil:<tag>

(see `toil/tags`_ for valid values for ``<tag>``)

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