recipe bamslice

Extract byte ranges from BAM files and convert to interleaved FASTQ format for parallel processing

Homepage:

https://github.com/nebiolabs/bamslice

Documentation:

https://docs.rs/bamslice

License:

AGPL / AGPL-3.0-only

Recipe:

/bamslice/meta.yaml

Links:

biotools: bamslice

bamslice extracts specific byte ranges from BAM files and converts them to interleaved FASTQ format. Designed for parallel processing across compute nodes without requiring pre-indexing. It auto-aligns to BGZF block boundaries and guarantees no duplicate reads when using contiguous byte ranges.

package bamslice

(downloads) docker_bamslice

versions:

0.1.0-0

depends bzip2:

>=1.0.8,<2.0a0

depends libcurl:

>=8.16.0,<9.0a0

depends libdeflate:

>=1.22,<1.23.0a0

depends libgcc:

>=13

depends liblzma:

>=5.8.1,<6.0a0

depends libzlib:

>=1.3.1,<2.0a0

depends openssl:

>=3.5.4,<4.0a0

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 bamslice

and update with::

   mamba update bamslice

To create a new environment, run:

mamba create --name myenvname bamslice

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/bamslice:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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