recipe cromshell

Command-line interface to the Cromwell workflow manager

Homepage:

https://github.com/broadinstitute/cromshell

License:

BSD / BSD-3-Clause

Recipe:

/cromshell/meta.yaml

package cromshell

versions:

2.1.1-0,  2.1.0-0,  2.0.0-0,  0.5.3-0,  0.5.2-0,  0.5.1-0,  0.5.0-0,  0.4.4-0,  0.4.3-1, 

2.1.1-0,  2.1.0-0,  2.0.0-0,  0.5.3-0,  0.5.2-0,  0.5.1-0,  0.5.0-0,  0.4.4-0,  0.4.3-1,  0.4.3-0,  0.4.2-0,  0.4.1-0,  0.4.0-0,  0.3.12-0,  0.3.11-0,  0.3.10-1,  0.3.10-0,  0.3.9-0,  0.3.8-0,  0.3.6-0,  0.3.4-0,  0.3.3-0,  0.2.3-0

depends click:

>=8

depends gcsfs:

>=2022.3.0

depends google-cloud-bigquery:

>=3.5.0

depends jq:

depends pygments:

>=2.12.0

depends python:

>=3

depends requests:

>=2.27.1

depends tabulate:

>=0.8.9

depends termcolor:

>=1.1.0

depends womtool:

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 cromshell

and update with::

   mamba update cromshell

To create a new environment, run:

mamba create --name myenvname cromshell

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/cromshell:<tag>

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

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