-3
#!/bin/bash

./bbmap.sh ref=ref.fa # creating index file from the input  

for $i in {ls*.fastq} # trying to run batch processing 
do
    ./bbmap.sh in=$i out={.}
done

It says:

BBMap version 35.74
Retaining first best site only for ambiguous mappings.
No output file.
NOTE:   Ignoring reference file because it already appears to have been processed.
NOTE:   If you wish to regenerate the index, please manually delete ref/genome/1/summary.txt
Set genome to 1

Loaded Reference:   3.390 seconds.
Loading index for chunk 1-2, build 1
Generated Index:    1.011 seconds.
No reads to process; quitting.

Total time:         4.443 seconds.
TestScript.sh: line 6: `$i': not a valid identifier
  • 3
    Too much $ for once :) drop the $ from for $i... – Jeff Schaller Jan 1 '16 at 19:41
1

Pass them on the command line and reference them with $1, $2, etc, in your script.

0

You should change for $i in {ls*.fastq} # trying to run batch processing to for i in {ls*.fastq} # trying to run batch processing, because by using $i when declaring the loop, bash replaced $i with a blank space, as you hadn't previously assigned it a value.

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