Bash Running scripts for DIAMOND and DAA-MEGANIZER


#1

Here is my script for running DIAMOND on a server, please see DIAMOND help for more details:

#!/bin/bash
if [ $# != “2” ]
then
echo “Usage: run-diamond.sh infile outfile”
exit 1
fi
echo “time ~/software/diamond blastx -b 20 -t /dev/shm --db /abprojects/daniel/nr/nr-Jan2017/nr --out $2 --outfmt 100 --query $1”
time ~/software/diamond blastx -b 20 -t /dev/shm --db /abprojects/daniel/nr/nr-Jan2017/nr --out $2 --outfmt 100 --query $1


#2

Here is my script for running DAA-MEGANIZER for shoer reads on a server, please see daa-meganizer -h for more details:

#/bin/bash
if [ $# != 1 ]
then
echo “Usage: meganize daa-file"
exit 1
fi
input=”-i $1"
options="-v -fun EGGNOG KEGG INTERPRO2GO SEED --parseTaxonNames false"
mapping="/home3/daniel/mapping"
tax="-a2t $mapping/prot_acc2tax-Nov2016X.abin"
kegg="-a2kegg $mapping/acc2kegg-Nov2016X-ue.abin"
eggnog="-a2eggnog $mapping/acc2eggnog-Nov2016X.abin"
interpro="-a2interpro2go $mapping/acc2interpro-Nov2016XX.abin"
seed="-a2seed $mapping/acc2seed-May2015XX.abin"
~/software/megan6ue/tools/daa-meganizer $input $options $tax $kegg $eggnog $interpro $seed