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Problems with GNU parallel


From: Ole Tange
Subject: Re: Problems with GNU parallel
Date: Fri, 21 Jan 2011 15:21:14 +0100 
Hi Ravio.

Consider using the email list for support:
http://lists.gnu.org/mailman/listinfo/parallel then you are not
dependent on me alone.

Your problem is caused by one of the features in GNU Parallel:
arguments containing spaces are quoted so they appear to be a single
argument. This is usually what you when when you are dealing with
filenames containing spaces.

What you want is to pass multiple arguments and have the space be
evaulated by the shell.

In your case the solution is easy: Simply pass the whole command to
parallel instead of just the arguments:

echo "bigWigSummary Ser2.bw chr1 1119999 1129999 1 -type=mean" | parallel

In this situation GNU Parallel will not interpret the input as
arguments but as a complete command line and therefore the spaces will
be evaluated by the shell.

So just put 'bigWigSummary' on the start of every line and do:

cat test.txt |  parallel  -k

A good test to see if GNU Parallel quotes the spaces is to use:

"two  spaces"

as argument. If the two spaces between 'two' and 'spaces' are kept
then the spaces have been quoted. If there is only one space left then
it was evaluated by the shell. E.g.

echo "echo two  spaces" | parallel

echo "echo two  spaces" | parallel echo


/Ole

On Fri, Jan 21, 2011 at 2:54 PM, Raivo Kolde
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