Package Recipe 'bcbio-nextgen-vm'

recipe bcbio-nextgen-vm

Run bcbio-nextgen genomic sequencing analyses using isolated containers and virtual machines

Homepage:: https://github.com/chapmanb/bcbio-nextgen-vm
License:: MIT
Recipe:: /bcbio-nextgen-vm/meta.yaml

package bcbio-nextgen-vm¶

Versions:

0.1.6-3, 0.1.6-2, 0.1.6-1, 0.1.6-0, 0.1.5-0, 0.1.3-1, 0.1.2a-1, 0.1.1-1, 0.1.1-0,

0.1.6-3, 0.1.6-2, 0.1.6-1, 0.1.6-0, 0.1.5-0, 0.1.3-1, 0.1.2a-1, 0.1.1-1, 0.1.1-0, 0.1.0a-136, 0.1.0a-135, 0.1.0a-134, 0.1.0a-133, 0.1.0a-132, 0.1.0a-131, 0.1.0a-130, 0.1.0a-129, 0.1.0a-128, 0.1.0a-127, 0.1.0a-126, 0.1.0a-125, 0.1.0a-124, 0.1.0a-123, 0.1.0a-122, 0.1.0a-121, 0.1.0a-120, 0.1.0a-119, 0.1.0a-118, 0.1.0a-117, 0.1.0a-116, 0.1.0a-115, 0.1.0a-114, 0.1.0a-113, 0.1.0a-112, 0.1.0a-111, 0.1.0a-110, 0.1.0a-109, 0.1.0a-108, 0.1.0a-107, 0.1.0a-106, 0.1.0a-105, 0.1.0a-104, 0.1.0a-103, 0.1.0a-102, 0.1.0a-101, 0.1.0a-100, 0.1.0a-99, 0.1.0a-98, 0.1.0a-97, 0.1.0a-96, 0.1.0a-95, 0.1.0a-94, 0.1.0a-93, 0.1.0a-92, 0.1.0a-91, 0.1.0a-90, 0.1.0a-89, 0.1.0a-88, 0.1.0a-87, 0.1.0a-86, 0.1.0a-85, 0.1.0a-84, 0.1.0a-83, 0.1.0a-82, 0.1.0a-81, 0.1.0a-80, 0.1.0a-79, 0.1.0a-78, 0.1.0a-77, 0.1.0a-76, 0.1.0a-75, 0.1.0a-74, 0.1.0a-73, 0.1.0a-72, 0.1.0a-71, 0.1.0a-70, 0.1.0a-69

Depends:

on arvados-cwl-runner >=1.3.1.20190301150258
on bcbio-nextgen >1.1.4
on boto3
on cachecontrol 0.11.7
on cromwell >=0.36
on cwltool
on dx-cwl >=0.1.0a20180820
on dxpy
on google-cloud-sdk
on ipyparallel >=6.0.2
on nodejs
on nose
on pathlib2 2.3.2
on pysam >=0.15.2
on python
on python-dateutil >=2.5.0
on rabix-bunny >=1.0.4
on ruamel.yaml >=0.13.0
on sevenbridges-python >=0.17.5
on six
on synapseclient

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bcbio-nextgen-vm

to add into an existing workspace instead, run:

pixi add bcbio-nextgen-vm

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bcbio-nextgen-vm

Alternatively, to install into a new environment, run:

conda create -n envname bcbio-nextgen-vm

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bcbio-nextgen-vm:<tag>

(see bcbio-nextgen-vm/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bcbio-nextgen-vm/README.html)