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I have a short bash script running samtools mpileup. It works fine locally, but when I try run it on SGE, I get an “illegal variable name” feedback.
#!/bin/bash
for f in $(find /bed_files -name '*.bed' )
do
name=$(echo $f | awk 'gsub("/", "_")')
name2=$(echo $name | awk 'gsub("_bed_files_", "")')
name3=$(echo $name2 | awk 'gsub(".bed", "")')
samtools runs here
done
Is SGE variable syntax different to bash?
Yes, I needed to change the first line to: