:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'funannotate' .. highlight: bash funannotate =========== .. conda:recipe:: funannotate :replaces_section_title: :noindex: 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: :biotools:`funannotate`, usegalaxy-eu: :usegalaxy-eu:`funannotate_compare`, usegalaxy-eu: :usegalaxy-eu:`funannotate_clean`, usegalaxy-eu: :usegalaxy-eu:`funannotate_predict`, usegalaxy-eu: :usegalaxy-eu:`funannotate_annotate` .. conda:package:: funannotate |downloads_funannotate| |docker_funannotate| :versions: .. raw:: html
1.8.17-11.8.17-01.8.15-21.8.15-11.8.15-01.8.13-01.8.11-01.8.9-31.8.9-2 ``1.8.17-1``,  ``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`` .. raw:: html
:depends augustus: ``3.5.0`` :depends bamtools: :depends bedtools: :depends biopython: ``<1.80`` :depends blast: :depends codingquarry: :depends diamond: :depends distro: :depends ete3: :depends evidencemodeler: ``1.1.1`` :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 phyml: :depends pigz: :depends proteinortho: :depends psutil: :depends python: ``>=3.6,<3.10`` :depends raxml: :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: :additional platforms: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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: (see `funannotate/tags`_ for valid values for ````) .. |downloads_funannotate| image:: https://img.shields.io/conda/dn/bioconda/funannotate.svg?style=flat :target: https://anaconda.org/bioconda/funannotate :alt: (downloads) .. |docker_funannotate| image:: https://quay.io/repository/biocontainers/funannotate/status :target: https://quay.io/repository/biocontainers/funannotate .. _`funannotate/tags`: https://quay.io/repository/biocontainers/funannotate?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/funannotate/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/funannotate/README.html