recipe nullarbor

Pipeline to generate complete public health microbiology reports from sequenced isolates

Homepage

https://github.com/tseemann/nullarbor

License

GPL2

Recipe

/nullarbor/meta.yaml

package nullarbor

(downloads) docker_nullarbor

Versions

2.0.20181010-4, 2.0.20181010-2

Depends abricate

>=0.8

Depends bwa

>=0.7.17

Depends centrifuge

>=1.0

Depends fasttree

Depends flash

>=1.2

Depends iqtree

>=1.6

Depends kraken

>=1.1

Depends kraken2

Depends lighter

>=1.1

Depends mash

>=2.1

Depends megahit

>=1.1

Depends mlst

>=2.1

Depends newick_utils

Depends perl

Depends perl-file-spec

Depends perl-findbin

Depends perl-path-tiny

Depends perl-yaml-tiny

Depends pigz

Depends pilon

>=1.22

Depends prokka

>=1.12

Depends quicktree

>=2.4

Depends roary

>=3.0

Depends samclip

>=0.2

Depends samtools

>=1.8

Depends seqtk

>=1.3

Depends shovill

>=1.0

Depends skesa

>=2.3

Depends snippy

>=4.2

Depends snp-dists

>=0.6

Depends spades

>=3.6

Depends trimmomatic

>=0.36

Depends velvet

>=1.2.10

Requirements

Installation

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

conda install nullarbor

and update with:

conda update nullarbor

or use the docker container:

docker pull quay.io/biocontainers/nullarbor:<tag>

(see nullarbor/tags for valid values for <tag>)