Package Recipe 'bcbio-nextgen'

recipe bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

Homepage:: https://github.com/bcbio/bcbio-nextgen
License:: MIT
Recipe:: /bcbio-nextgen/meta.yaml
Links:: biotools: bcbio-nextgen

package bcbio-nextgen¶

Versions:

1.2.9-3, 1.2.9-2, 1.2.9-1, 1.2.9-0, 1.2.8-0, 1.2.7-0, 1.2.6-0, 1.2.5-0, 1.2.4-0,

1.2.9-3, 1.2.9-2, 1.2.9-1, 1.2.9-0, 1.2.8-0, 1.2.7-0, 1.2.6-0, 1.2.5-0, 1.2.4-0, 1.2.3-1, 1.2.3-0, 1.2.2-0, 1.2.1-0, 1.2.0-0, 1.1.9-0, 1.1.8-0, 1.1.7-0, 1.1.6-0, 1.1.6a-1, 1.1.6a-0, 1.1.5-0, 1.1.5a-1, 1.1.5a-0, 1.1.4-0, 1.1.4a-3, 1.1.4a-2, 1.1.4a-1, 1.1.4a-0, 1.1.3-0, 1.1.3a-4, 1.1.3a-3, 1.1.3a-2, 1.1.3a-1, 1.1.3a-0, 1.1.2-0, 1.1.2a-3, 1.1.2a-2, 1.1.2a-1, 1.1.2a-0, 1.1.1-0, 1.1.1a-12, 1.1.1a-11, 1.1.1a-10, 1.1.1a-9, 1.1.1a-8, 1.1.1a-7, 1.1.1a-6, 1.1.1a-5, 1.1.1a-4, 1.1.1a-3, 1.1.1a-2, 1.1.1a-1, 1.1.1a-0, 1.1.0-0, 1.1.0a-11, 1.1.0a-8, 1.1.0a-7, 1.1.0a-6, 1.1.0a-5, 1.1.0a-4, 1.1.0a-3, 1.1.0a-2, 1.1.0a-1, 1.1.0a-0, 1.0.9-0, 1.0.9a-9, 1.0.9a-8, 1.0.9a-7, 1.0.9a-6, 1.0.9a-5, 1.0.9a-4, 1.0.9a-3, 1.0.9a-2, 1.0.9a-1, 1.0.9a-0, 1.0.8-0, 1.0.8a-5, 1.0.8a-4, 1.0.8a-3, 1.0.8a-2, 1.0.8a-1, 1.0.8a-0, 1.0.7-1, 1.0.7-0, 1.0.7a0-7, 1.0.7a0-6, 1.0.7a0-5, 1.0.7a0-4, 1.0.7a0-3, 1.0.7a0-2, 1.0.7a0-1, 1.0.7a0-0, 1.0.6-0, 1.0.6a0-6, 1.0.6a0-5, 1.0.6a0-4, 1.0.6a0-3, 1.0.6a0-2, 1.0.6a0-1, 1.0.6a0-0, 1.0.5-0, 1.0.5a-6, 1.0.5a-5, 1.0.5a-4, 1.0.5a-3, 1.0.5a-2, 1.0.5a-1, 1.0.5a-0, 1.0.4-0, 1.0.4a0-3, 1.0.4a0-2, 1.0.4a0-1, 1.0.4a0-0, 1.0.3-0, 1.0.3a-10, 1.0.3a-9, 1.0.3a-8, 1.0.3a-7, 1.0.3a-6, 1.0.3a-5, 1.0.3a-4, 1.0.3a-3, 1.0.3a-2, 1.0.3a-1, 1.0.3a-0, 1.0.2-0, 1.0.2a-1, 1.0.2a-0, 1.0.1-1, 1.0.1-0, 1.0.1a0-4, 1.0.1a0-3, 1.0.1a0-2, 1.0.1a0-1, 1.0.1a0-0, 1.0.0-0, 1.0.0a0-8, 1.0.0a0-7, 1.0.0a0-6, 1.0.0a0-5, 1.0.0a0-4, 1.0.0a0-3, 1.0.0a0-1, 1.0.0a0-0, 0.9.9-0, 0.9.9a0-4, 0.9.9a0-3, 0.9.9a0-2, 0.9.9a0-1, 0.9.9a0-0, 0.9.8-0, 0.9.8a0-7, 0.9.8a0-6, 0.9.8a0-5, 0.9.8a0-4, 0.9.8a0-3, 0.9.8a0-2, 0.9.8a0-1, 0.9.8a0-0, 0.9.7-0, 0.9.7a-5, 0.9.7a-4, 0.9.7a-3, 0.9.7a-2, 0.9.7a-1, 0.9.7a-0, 0.9.6-0, 0.9.6a-3, 0.9.6a-2, 0.9.6a-1, 0.9.6a-0, 0.9.5-1

Depends:

on arrow
on beautifulsoup4
on bioblend
on biopython
on boto
on cyvcf2
on dnapi
on fadapa
on geneimpacts
on gffutils
on h5py
on htslib
on ipyparallel 6.3.0.*
on ipython-cluster-helper 0.6.4 py_0
on joblib >=0.12
on logbook
on matplotlib-base
on mock
on msgpack-python
on openssl <3.0.0
on pandas
on pip
on psutil
on py
on pybedtools
on pycrypto
on pysam >=0.13.0
on pytest
on pytest-cov >=2.6.1
on pytest-mock
on python
on python-dateutil >=2.5.0
on pyvcf
on pyyaml
on requests
on scipy >=1.3.0
on seaborn
on seqcluster
on statsmodels
on tabulate
on toolz
on yamllint

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

to add into an existing workspace instead, run:

pixi add bcbio-nextgen

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

Alternatively, to install into a new environment, run:

conda create -n envname bcbio-nextgen

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:<tag>

(see bcbio-nextgen/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/README.html)