recipe tigmint

Correct misassemblies using linked or long reads

Homepage:

https://bcgsc.github.io/tigmint/

Documentation:

https://github.com/bcgsc/tigmint#readme

Developer docs:

https://github.com/bcgsc/tigmint

License:

GPL-3.0

Recipe:

/tigmint/meta.yaml

Links:

doi: 10.1101/304253

package tigmint

versions:

1.2.10-4,  1.2.10-3,  1.2.10-2,  1.2.10-1,  1.2.10-0,  1.2.9-2,  1.2.9-1,  1.2.9-0,  1.2.8-0, 

1.2.10-4,  1.2.10-3,  1.2.10-2,  1.2.10-1,  1.2.10-0,  1.2.9-2,  1.2.9-1,  1.2.9-0,  1.2.8-0,  1.2.7-0,  1.2.6-3,  1.2.6-2,  1.2.6-1,  1.2.6-0,  1.2.5-1,  1.2.5-0,  1.2.4-1,  1.2.4-0,  1.2.3-0,  1.2.2-1,  1.2.2-0,  1.2.1-0,  1.1.2-0

depends _openmp_mutex:

>=4.5

depends btllib:

>=1.7.3,<2.0a0

depends bwa:

depends intervaltree:

depends libgcc:

>=13

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

depends make:

depends minimap2:

depends pybedtools:

depends pysam:

>=0.15.3

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends samtools:

depends zsh:

requirements:

additional platforms:

linux-aarch64,  osx-arm64

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 tigmint

and update with::

   mamba update tigmint

To create a new environment, run:

mamba create --name myenvname tigmint

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/tigmint:<tag>

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

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