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paths.sh
executable file
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paths.sh
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#!/bin/bash -ex
function abspath() {
if [ -d "$1" ]; then
(cd "$1"; pwd)
elif [ -f "$1" ]; then
if [[ $1 == */* ]]; then
echo "$(cd "${1%/*}"; pwd)/${1##*/}"
else
echo "$(pwd)/$1"
fi
fi
}
SCRIPTPATH="$( cd $(dirname $0) ; pwd )"
HHDBPATH="/cbscratch/mmirdit/databases"
MMDIR="/cbscratch/mmirdit/uniclust/pipeline/mmseqs"
PATH="$MMDIR/bin:$MMDIR/util:$PATH"
HHLIB="/cbscratch/mmirdit/uniclust/pipeline/hh-suite"
PATH="$HHLIB/bin:$HHLIB/scripts:$PATH"
HHDB="${SCRIPTPATH}/hhdatabase"
PATH="$HHDB:$PATH"
UCDIR="${SCRIPTPATH}"
PATH="$UCDIR:$UCDIR/annotation:$PATH"
export FASTA="./input.fasta"
export RELEASE="2016_09"
export SHORTRELEASE="1609"
export BASE="output"
export TARGET="$(abspath ./output/${RELEASE})"
export PATH
export MMDIR
export HHLIB
export HHDB
export HHDBPATH
export OMPI_MCA_btl_openib_ib_timeout=31
function hasCommand() {
command -v $1 >/dev/null 2>&1 || { echo "Please make sure that $1 is in \$PATH."; exit 1; }
}
hasCommand mmseqs
hasCommand awk
hasCommand tar
hasCommand pigz
hasCommand cstranslate_mpi
if [[ ! -e ${HHLIB}/data/cs219.lib ]] || [[ ! -e ${HHLIB}/data/context_data.lib ]]; then
echo "Missing required cstranslate data, check HHLIB env var!"
exit 1;
fi
hasCommand sed
hasCommand md5deep
hasCommand clustalo
hasCommand kalign
hasCommand timeout
hasCommand python
hasCommand python3
hasCommand hhblits_mpi