dear ole, if you have read (http://en.wikipedia.org/wiki/Reading_%28process%29) the problem accurately you would have recognised, that it is a simple problem, not the command per se doesn't work, but it doesn't work from inside a script: it seems that you have to export the command (this is not very well documented). this you could have advised without instructing users how to write error reports...
dietmar On 12/17/2012 01:23 AM, Ole Tange wrote: > On Thu, Dec 6, 2012 at 9:04 PM, Dietmar Pils <[email protected]> > 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.
