recipe shovill

Microbial assembly pipeline for Illumina paired-end reads

Homepage:

https://github.com/tseemann/shovill

License:

GPL2

Recipe:

/shovill/meta.yaml

Links:

biotools: shovill, usegalaxy-eu: shovill

package shovill

(downloads) docker_shovill

versions:
1.1.0-11.1.0-01.0.9-01.0.4-11.0.4-01.0.1-01.0.0-00.9.0-10.9.0-0

1.1.0-11.1.0-01.0.9-01.0.4-11.0.4-01.0.1-01.0.0-00.9.0-10.9.0-00.8.0-00.7.1-20.7.1-10.7.1-0

depends bwa:

>=0.7.17

depends flash:

>=1.2

depends kmc:

>=3.1

depends lighter:

>=1.1

depends megahit:

>=1.2.7

depends perl:

depends perl-file-spec:

depends perl-findbin:

depends pigz:

depends pilon:

>=1.22

depends samclip:

>=0.4

depends samtools:

>=1.10

depends seqtk:

>=1.3

depends skesa:

>=2.2

depends spades:

>=3.14

depends trimmomatic:

>=0.36

depends velvet:

>=1.2.10

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 shovill

and update with::

   mamba update shovill

To create a new environment, run:

mamba create --name myenvname shovill

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/shovill:<tag>

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

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