recipe crossmap

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: crossmap_bam, usegalaxy-eu: crossmap_bed, usegalaxy-eu: crossmap_vcf, usegalaxy-eu: crossmap_wig, usegalaxy-eu: crossmap_gff, doi: 10.1093/bioinformatics/btt730, biotools: crossmap

package crossmap

(downloads) docker_crossmap

versions:
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, 

0.7.0-0,  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

depends bx-python:

depends numpy:

depends pybigwig:

depends pysam:

>=0.15

depends python:

>=3.8

depends ucsc-wigtobigwig:

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 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:<tag>

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

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