recipe dragonflye

Microbial assembly pipeline for Nanopore reads

Homepage:

https://github.com/rpetit3/dragonflye

License:

GPL2

Recipe:

/dragonflye/meta.yaml

Links:

biotools: dragonflye, usegalaxy-eu: dragonflye

package dragonflye

versions:

1.2.1-0,  1.2.0-0,  1.1.2-0,  1.1.1-0,  1.1.0-0,  1.0.14-0,  1.0.13-0,  1.0.12-0,  1.0.11-0, 

1.2.1-0,  1.2.0-0,  1.1.2-0,  1.1.1-0,  1.1.0-0,  1.0.14-0,  1.0.13-0,  1.0.12-0,  1.0.11-0,  1.0.10-0,  1.0.9-0,  1.0.8-0,  1.0.7-0,  1.0.6-0,  1.0.5-0,  1.0.4-0,  1.0.3-0,  1.0.2-0,  1.0.1-0,  1.0.0-0

depends any2fasta:

>=0.4.2

depends assembly-scan:

>=1.0.0

depends bwa:

depends dnaapler:

depends fastp:

depends flye:

>=2.9.2

depends kmc:

>=3.1

depends medaka:

>=1.11.0

depends miniasm:

>=0.3_r179

depends nanoq:

>=0.10.0

depends perl:

>=5.26

depends perl-file-spec:

depends perl-findbin:

depends pigz:

>=2.6

depends pilon:

depends polypolish:

>=0.6.0

depends porechop:

depends racon:

>=1.5.0

depends rasusa:

>=1.0.0

depends raven-assembler:

>=1.8.3

depends samclip:

depends samtools:

depends seqtk:

>=1.4

requirements:

additional platforms:

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 dragonflye

and update with::

   mamba update dragonflye

To create a new environment, run:

mamba create --name myenvname dragonflye

with myenvname being 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/dragonflye:<tag>

(see `dragonflye/tags`_ for valid values for ``<tag>``)

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