bash question

[OBBARD Darren]

Hi all,

This bash loop works for one user on a machine, but not for another, when pasted into the terminal (note the indenting)

for F in *_1.fastq.gz;
do
stem=$(echo $F | sed 's/_.\+//');
cutadapt -a AGATCGGAAGAGCACACGTCTG -A AGATCGGAAGAGCGTCGTGTAG -o ${stem}_1.trim.fastq -p ${stem}_2.trim.fastq ${stem}_1.fastq.gz ${stem}_2.fastq.gz;
gzip ${stem}_1.trim.fastq &
gzip ${stem}_2.trim.fastq &
done

For both users, echo $SHELL returns "/bin/bash"

The following loop works for both users when pasted into the terminal (note different indenting

for F in *_1.fastq.gz;
do
stem=$(echo $F | sed 's/_.\+//');
cutadapt -a AGATCGGAAGAGCACACGTCTG -A AGATCGGAAGAGCGTCGTGTAG -o ${stem}_1.trim.fastq -p ${stem}_2.trim.fastq ${stem}_1.fastq.gz ${stem}_2.fastq.gz;
gzip ${stem}_1.trim.fastq &
gzip ${stem}_2.trim.fastq &
done

but *both* versions work when placed in a shell script and invoked with

bash ./ThisScript.sh

Why is this?

Thanks,

D.


--
Darren Obbard
darren...@ed.ac.uk

Institute of Evolutionary Biology
University of Edinburgh
Room 2.09, Ashworth 2, Charlotte Auerbach Road
EdinburghEH9 3FL

Office 0131 651 7781
Mobile: 07968 838 635

http://obbard.bio.ed.ac.uk/
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[OBBARD Darren]

Ignore that - I still don't know why it works, but the mail client has stripped all the tabs and half the newlines, making my email unintelligible

--
Darren Obbard
darren...@ed.ac.uk

Institute of Evolutionary Biology
University of Edinburgh
Room 2.09, Ashworth 2, Charlotte Auerbach Road

Edinburgh EH9 3FL

Office 0131 651 7781
Mobile: 07968 838 635

http://obbard.bio.ed.ac.uk/
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