:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'itero' .. highlight: bash itero ===== .. conda:recipe:: itero :replaces_section_title: :noindex: A pipeline for iterative\, guided contig assembly that integrates spades\, bwa\, and samtools to produce assembled contigs. :homepage: https://github.com/faircloth-lab/itero :license: BSD :recipe: /`itero `_/`meta.yaml `_ .. conda:package:: itero |downloads_itero| |docker_itero| :versions: ``1.1.2-1``,  ``1.1.2-0``,  ``1.1.1-2``,  ``1.1.1-0``,  ``1.1.0-0``,  ``1.0.1-0``,  ``1.0.0-0`` :depends argcomplete: :depends bedtools: :depends biopython: :depends bwa: :depends gawk: :depends grep: :depends mpi4py: :depends nomkl: :depends numpy: :depends python: ``<3`` :depends samtools: :depends schwimmbad: :depends six: :depends spades: ``3.12.*`` :requirements: .. 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 itero and update with:: mamba update itero To create a new environment, run:: mamba create --name myenvname itero 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/itero: (see `itero/tags`_ for valid values for ````) .. |downloads_itero| image:: https://img.shields.io/conda/dn/bioconda/itero.svg?style=flat :target: https://anaconda.org/bioconda/itero :alt: (downloads) .. |docker_itero| image:: https://quay.io/repository/biocontainers/itero/status :target: https://quay.io/repository/biocontainers/itero .. _`itero/tags`: https://quay.io/repository/biocontainers/itero?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/itero/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/itero/README.html