Merging STDIN and STDOUT in a gridengine submission

We recently hit a problem when trying to run a fairly simple script through grid engine.  The script used an internal redirection to merge together STDIN and STDOUT before doing a final transformation on the result. A simplified version of what the script did is something like this: echo hello 2>&1 | sed s/^/prefix:/  …

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Published:July 8, 2014 View Post

Bioinformatics Computing

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Overestimating DWIM in Perl

I hit a bug in a script I was writing this week which reminded me that sometimes you can put too much faith in perl’s ability to ‘do what I mean’ (DWIM). It took me a couple of minutes to see what was going wrong here – see if you do any better. #!/usr/bin/perl use…

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Published:October 17, 2009 View Post

Computing

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