recipe ngs-smap

SMAP is an analysis tool for stack-based NGS read mapping

Homepage:

https://gitlab.com/truttink/smap

License:

GPL3 / GPL-3.0-or-later

Recipe:

/ngs-smap/meta.yaml

package ngs-smap

versions:

5.0.1-0,  4.6.5-0,  4.6.4-0,  4.6.2-0,  4.6.1-0,  4.6.0-0,  4.5.1-0,  4.5.0-0

depends biopython:

>=1.8

depends colorlog:

>=6.6.0,<6.7

depends cutadapt:

4.4

depends gffpandas:

1.2.*

depends gffutils:

depends matplotlib-base:

>=3.5.1,<3.6

depends natsort:

8.2.0

depends numexpr:

depends openpyxl:

>=3.0.9,<3.1.0

depends pandas:

>=2.0.3,<2.1.0

depends plotly:

>=5.5

depends primer3-py:

depends pybedtools:

>=0.9.0,<0.10

depends pysam:

>=0.22.0,<0.23.0

depends python:

>=3.8.1,!=3.11

depends scipy:

depends seaborn:

0.12.1

depends tqdm:

depends typing-extensions:

>=4.0.0,<4.1.1

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 ngs-smap

and update with::

   mamba update ngs-smap

To create a new environment, run:

mamba create --name myenvname ngs-smap

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/ngs-smap:<tag>

(see `ngs-smap/tags`_ for valid values for ``<tag>``)

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Link to this page

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