recipe funannotate

funannotate: eukaryotic genome annotation pipeline

Homepage:

https://github.com/nextgenusfs/funannotate

Documentation:

https://funannotate.readthedocs.io/en/latest/

License:

BSD / BSD-2-Clause

Recipe:

/funannotate/meta.yaml

Links:

biotools: funannotate, usegalaxy-eu: funannotate_compare, usegalaxy-eu: funannotate_clean, usegalaxy-eu: funannotate_predict, usegalaxy-eu: funannotate_annotate

package funannotate

versions:

1.8.17-0,  1.8.15-2,  1.8.15-1,  1.8.15-0,  1.8.13-0,  1.8.11-0,  1.8.9-3,  1.8.9-2,  1.8.9-1, 

1.8.17-0,  1.8.15-2,  1.8.15-1,  1.8.15-0,  1.8.13-0,  1.8.11-0,  1.8.9-3,  1.8.9-2,  1.8.9-1,  1.8.9-0,  1.8.7-0,  1.8.5-1,  1.8.5-0,  1.8.3-0,  1.8.1-1,  1.8.1-0,  1.7.4-1,  1.7.4-0,  1.7.3-0,  1.7.2-0,  1.7.1-1

depends augustus:

3.5.0

depends bamtools:

depends bedtools:

depends biopython:

<1.80

depends blast:

depends codingquarry:

depends diamond:

depends ete3:

depends evidencemodeler:

depends exonerate:

depends fasta3:

depends glimmerhmm:

depends goatools:

depends hisat2:

depends hmmer:

depends kallisto:

>=0.46.0,<0.46.2

depends mafft:

>=7

depends matplotlib-base:

depends minimap2:

depends natsort:

depends numpy:

depends pandas:

depends pasa:

depends perl:

depends perl-clone:

depends perl-db_file:

depends perl-dbd-mysql:

depends perl-hash-merge:

depends perl-json:

depends perl-local-lib:

depends perl-logger-simple:

depends perl-math-utils:

depends perl-mce:

depends perl-parallel-forkmanager:

depends perl-scalar-util-numeric:

depends perl-soap-lite:

depends perl-text-soundex:

depends pigz:

depends proteinortho:

depends psutil:

depends python:

>=3.6,<3.10

depends requests:

depends salmon:

depends samtools:

depends scikit-learn:

depends scipy:

depends seaborn-base:

depends snap:

depends stringtie:

depends tantan:

depends tbl2asn:

depends trimal:

depends trimmomatic:

depends trinity:

depends trnascan-se:

depends ucsc-blat:

depends ucsc-pslcdnafilter:

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 funannotate

and update with::

   mamba update funannotate

To create a new environment, run:

mamba create --name myenvname funannotate

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/funannotate:<tag>

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

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