recipe parasail

Pairwise Sequence Alignment Library

Homepage:

https://github.com/jeffdaily/parasail

License:

MIT / MIT

Recipe:

/parasail/meta.yaml

Links:

doi: 10.1186/s12859-016-0930-z

parasail is a SIMD C (C99) library containing implementations of the Smith-Waterman (local), Needleman-Wunsch (global), and various semi-global pairwise sequence alignment algorithms. Here, semi-global means insertions before the start or after the end of either the query or target sequence are optionally not penalized. parasail implements most known algorithms for vectorized pairwise sequence alignment, including diagonal [Wozniak, 1997], blocked [Rognes and Seeberg, 2000], striped [Farrar, 2007], and prefix scan [Daily, 2015]. Therefore, parasail is a reference implementation for these algorithms in addition to providing an implementation of the best-performing algorithm(s) to date on today's most advanced CPUs.

package parasail

(downloads) docker_parasail

versions:

2.6.2-1,  2.6.2-0

depends _openmp_mutex:

>=4.5

depends libgcc:

>=13

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

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 parasail

and update with::

   mamba update parasail

To create a new environment, run:

mamba create --name myenvname parasail

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/parasail:<tag>

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

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