Wrapper for MMseqs2

mmseqs_wrapper.sh

#!/bin/bash

## MIT License

## Copyright (c) 2019 Ryan Moore

## Permission is hereby granted, free of charge, to any person obtaining a copy
## of this software and associated documentation files (the "Software"), to deal
## in the Software without restriction, including without limitation the rights
## to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
## copies of the Software, and to permit persons to whom the Software is
## furnished to do so, subject to the following conditions:

## The above copyright notice and this permission notice shall be included in all
## copies or substantial portions of the Software.

## THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
## IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
## FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
## AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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## OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
## SOFTWARE.

mmseqs_avx2=/home/moorer/software/MMseqs2_binaries/mmseqs2_avx2/bin/mmseqs
mmseqs_sse41=/home/moorer/software/MMseqs2_binaries/mmseqs2_sse41/bin/mmseqs

grep avx2 /proc/cpuinfo > /dev/null

if [ $? -eq 0 ]; then
    "$mmseqs_avx2" "$@"
else
    grep sse4_1 /proc/cpuinfo > /dev/null

    if [ $? -eq 0 ]; then
        "$mmseqs_sse41" "$@"
    else
        >&2 echo "ERROR -- you don't have sse4.1 or avx2.  MMseqs2 will not work!"
        exit 1
    fi
fi

Use this wrapper if you are running MMseqs2 on a computing cluster where some of the nodes have AVX2 instructions and some have SSE4.1.