Re: use of parallel in bash script

[Ole Tange]

On Thu, Dec 6, 2012 at 9:04 PM, Dietmar Pils <dietmar.pils@univie.ac.at> wrote:

> how can I use parallel in a bash script? what do I miss, but the snippet
>
> time cat RUM.sam | parallel --pipe --files -N 5184953 sort -k 3,3 -k 4,4n |
> parallel -mj1 sort -k 3,3 -k 4,4n -m {} ";" rm {} > sort.sam
>
> works from the command lane but not in a bash script.
>
> what have I to do, that I can run the same from inside a bash script...

You need to learn to write better error reports. See for instance:

http://www.ehow.com/how_6946968_write-error-report.html

One thing that article leaves out is: Try to minimize/simplify your
problem. If steps A B C D do not work, you need to let the programmer
know if A, A B, and A B C do work.


/Ole

PS: sort from GNU coreutils 8.6 uses multiple CPUs for sorting, so
using GNU Parallel for sorting is less efficient.