recipe htstream

HTStream is a quality control and processing pipeline for High Throughput Sequencing data. The difference between HTStream and other tools is that HTStream uses a tab delimited fastq format that allows for streaming from application to application. This streaming creates some awesome efficiencies when processing HTS data and makes it fully interoperable with other standard Linux tools.

Homepage:

https://s4hts.github.io/HTStream/

License:

Apache / Apache 2.0

Recipe:

/htstream/meta.yaml

package htstream

versions:

1.3.3-4,  1.3.3-3,  1.3.3-2,  1.3.3-1,  1.3.3-0,  1.3.2-0,  1.3.1-0,  1.2.0-0,  1.1.0-0, 

1.3.3-4,  1.3.3-3,  1.3.3-2,  1.3.3-1,  1.3.3-0,  1.3.2-0,  1.3.1-0,  1.2.0-0,  1.1.0-0,  1.0.0-0

depends boost:

>=1.78.0,<1.78.1.0a0

depends bzip2:

>=1.0.8,<2.0a0

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends libzlib:

>=1.2.13,<1.3.0a0

depends xz:

>=5.2.6,<6.0a0

depends zlib:

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 htstream

and update with::

   mamba update htstream

To create a new environment, run:

mamba create --name myenvname htstream

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/htstream:<tag>

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

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Link to this page

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