recipe gmcloser

GMcloser fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads.



GPL / GPL v3



package gmcloser

(downloads) docker_gmcloser



depends blast:

depends bowtie2:

depends mummer:

depends perl:

depends perl-findbin:

depends perl-getopt-long:

depends perl-pod-usage:



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 gmcloser

and update with::

   mamba update gmcloser

To create a new environment, run:

mamba create --name myenvname gmcloser

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<tag>

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

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