:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'crossmap' .. highlight: bash crossmap ======== .. conda:recipe:: crossmap :replaces_section_title: :noindex: CrossMap is a program for convenient conversion of genome coordinates and genomeannotation files between assemblies. :homepage: https://crossmap.sourceforge.net :documentation: https://crossmap.readthedocs.io/en/latest/ :developer docs: https://github.com/liguowang/CrossMap :license: GPL3 / GPL-3.0-or-later :recipe: /`crossmap `_/`meta.yaml `_ :links: usegalaxy-eu: :usegalaxy-eu:`crossmap_bam`, usegalaxy-eu: :usegalaxy-eu:`crossmap_bed`, usegalaxy-eu: :usegalaxy-eu:`crossmap_vcf`, usegalaxy-eu: :usegalaxy-eu:`crossmap_wig`, usegalaxy-eu: :usegalaxy-eu:`crossmap_gff`, doi: :doi:`10.1093/bioinformatics/btt730`, biotools: :biotools:`crossmap` .. conda:package:: crossmap |downloads_crossmap| |docker_crossmap| :versions: .. raw:: html
0.7.0-00.6.5-00.6.4-00.6.3-00.6.1-00.6.0-00.5.2-00.4.2-00.4.1-0 ``0.7.0-0``,  ``0.6.5-0``,  ``0.6.4-0``,  ``0.6.3-0``,  ``0.6.1-0``,  ``0.6.0-0``,  ``0.5.2-0``,  ``0.4.2-0``,  ``0.4.1-0``,  ``0.3.9-0``,  ``0.3.7-2``,  ``0.3.7-1``,  ``0.3.7-0``,  ``0.3.6-0``,  ``0.3.5-0``,  ``0.3.4-0``,  ``0.3.3-0``,  ``0.3.2-0``,  ``0.3.1-0``,  ``0.2.8-0``,  ``0.2.7-2``,  ``0.2.7-1``,  ``0.2.7-0``,  ``0.2.5-1``,  ``0.2.5-0``,  ``0.2.2-3``,  ``0.2.2-2``,  ``0.2.2-1``,  ``0.2.2-0``,  ``0.2.1-1``,  ``0.2.1-0`` .. raw:: html
:depends bx-python: :depends numpy: :depends pybigwig: :depends pysam: ``>=0.15`` :depends python: ``>=3.8`` :depends ucsc-wigtobigwig: :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 crossmap and update with:: mamba update crossmap To create a new environment, run:: mamba create --name myenvname crossmap 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/crossmap: (see `crossmap/tags`_ for valid values for ````) .. |downloads_crossmap| image:: https://img.shields.io/conda/dn/bioconda/crossmap.svg?style=flat :target: https://anaconda.org/bioconda/crossmap :alt: (downloads) .. |docker_crossmap| image:: https://quay.io/repository/biocontainers/crossmap/status :target: https://quay.io/repository/biocontainers/crossmap .. _`crossmap/tags`: https://quay.io/repository/biocontainers/crossmap?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/crossmap/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/crossmap/README.html