- recipe bcbio-nextgen
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
- Homepage:
- License:
MIT
- Recipe:
- 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 arrow:
- depends beautifulsoup4:
- depends bioblend:
- depends biopython:
- depends boto:
- depends cyvcf2:
- depends dnapi:
- depends fadapa:
- depends geneimpacts:
- depends gffutils:
- depends h5py:
- depends htslib:
- depends ipyparallel:
6.3.0.*- depends ipython-cluster-helper:
0.6.4 py_0- depends joblib:
>=0.12- depends logbook:
- depends matplotlib-base:
- depends mock:
- depends msgpack-python:
- depends openssl:
<3.0.0- 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:
- depends python-dateutil:
>=2.5.0- depends pyvcf:
- depends pyyaml:
- depends requests:
- depends scipy:
>=1.3.0- depends seaborn:
- depends seqcluster:
- depends statsmodels:
- depends tabulate:
- depends toolz:
- depends yamllint:
- 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 bcbio-nextgen and update with:: mamba update bcbio-nextgen
To create a new environment, run:
mamba create --name myenvname bcbio-nextgen
with
myenvnamebeing 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/bcbio-nextgen:<tag> (see `bcbio-nextgen/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bcbio-nextgen/README.html)
