/usr/share/ray/scripts/GenerateRayCommand.sh is in ray-extra 2.3.1-5.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 | echo "#Generated with $0 on $(date)"
echo "mpirun -np 30 /path/to/Ray \\"
for i in $(ls *.fast*|grep _1.fastq)
do
echo "-p \\"
echo " $(pwd)/$i \\"
echo " $(pwd)/$(echo $i|sed 's/_1\.fast/_2.fast/g') \\"
done
# BGI naming scheme in assemblathon 2
for i in $(ls *.fast*|grep _1.fq.fastq)
do
echo "-p \\"
echo " $(pwd)/$i \\"
echo " $(pwd)/$(echo $i|sed 's/_1\.fq.fast/_2.fq.fast/g') \\"
done
# assemblathon format
for i in $(ls *.fast*|grep "\.1\.fastq")
do
echo "-p \\"
echo " $(pwd)/$i \\"
echo " $(pwd)/$(echo $i|sed 's/\.1\.fast/.2.fast/g') \\"
done
output=$((ls *.fast*;date)|md5sum|awk '{print $1}')
echo "-o $output | tee $output"".log"
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