recipe bcbio-nextgen

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

Homepage

https://github.com/chapmanb/bcbio-nextgen

License

MIT

Recipe

/bcbio-nextgen/meta.yaml

Links

biotools: bcbio-nextgen

package bcbio-nextgen

(downloads) docker_bcbio-nextgen

Versions

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 arrow

Depends beautifulsoup4

Depends bioblend

Depends biopython

Depends boto

Depends cython

Depends cyvcf2

Depends dnapi

Depends fadapa

Depends geneimpacts

Depends gffutils

Depends h5py

Depends htslib

Depends ipyparallel

>=6.0.2

Depends ipython-cluster-helper

>=0.6.1

Depends joblib

>=0.12

Depends logbook

Depends matplotlib

Depends mock

Depends msgpack-python

Depends openssl

>=1.1.1b,<1.1.2a

Depends pandas

Depends pip

Depends psutil

Depends py

Depends pybedtools

Depends pycrypto

Depends pysam

>=0.13.0

Depends pytest

Depends pytest-cov

>=2.6.1

Depends pytest-mock

Depends python

>=2.7,<2.8.0a0

Depends python-dateutil

>=2.5.0

Depends pyvcf

Depends pyyaml

Depends requests

Depends scipy

Depends seaborn

Depends seqcluster

Depends statsmodels

Depends tabulate

Depends toolz

Depends yamllint

Requirements

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bcbio-nextgen

and update with:

conda update bcbio-nextgen

or use the docker container:

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

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