recipe hpcblast

A wrapper for NCBI-BLAST+ suite which provides a simple and efficient method to accelerate the blast search

Homepage:

https://github.com/yodeng/hpc-blast

License:

MIT / MIT

Recipe:

/hpcblast/meta.yaml

hpcblast provides a simple and efficient method for running the NCBI-BLAST+ suite program in localhost or the HPC environment (Sun Grid Engine). It splits the input sequence file and run all chunked tasks in parallel to accelerate the blast search speed. When there are many sequences in the input file for blast comparison and the running speed is slow, using hpcblast can significantly improve the performance. All of this can be easy done only by adding the hpc-blast command at the head of your blast command line.

package hpcblast

(downloads) docker_hpcblast

versions:

1.0.2-0

depends blast:

depends pip:

depends python:

>=3.5

depends runjob:

>=2.10.5

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 hpcblast

and update with::

   mamba update hpcblast

To create a new environment, run:

mamba create --name myenvname hpcblast

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/hpcblast:<tag>

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

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Link to this page

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