Hello Carrie,

Ganote, Carrie L wrote, On 03/27/2013 01:22 PM:
> 
> I am trying to upgrade our instance to the newest dist but I get the 
> following in stderr when I attempt to run Bowtie or BWA:
> 
> PREFIX/subs/galaxy_31.sh: command substitution: line 7: syntax error near 
> unexpected token `('
> PREFIX/subs/galaxy_31.sh: command substitution: line 7: `diff -n <(printf 
> "%s\n" "${LIST_BEFORE[@]}") <(printf "%s\n" "${LIST_AFTER[@]}") | tail -n +2'
> PREFIX/subs/galaxy_31.sh: command substitution: line 7: syntax error near 
> unexpected token `('
> PREFIX/subs/galaxy_31.sh: command substitution: line 7: `diff -n <(printf 
> "%s\n" "${LIST_BEFORE[@]}") <(printf "%s\n" "${LIST_AFTER[@]}") | tail -n +2'
> 
> The job is going to the cluster and coming back. The tool appears to run even 
> with the weird error. Sometimes the results are even correct, but I can't use 
> them due to the error state. Has anyone seen this error before?
> 

The immediate reason is that on your cluster, the shell (e.g. bash) runs in 
POSIX mode, and the "<()" construct isn't POSIX compatible.

Consider the following:
==
$ bash -c "cat <(printf 'hello world\n')"
hello world

$ dash -c "cat <(printf 'hello world\n')"
dash: 1: Syntax error: "(" unexpected

$ bash --posix -c "cat <(printf 'hello world\n')"
bash: -c: line 0: syntax error near unexpected token `('
bash: -c: line 0: `cat <(printf 'hello world\n')'

$ /bin/sh -c "cat <(printf 'hello world\n')"
/bin/sh: -c: line 0: syntax error near unexpected token `('
/bin/sh: -c: line 0: `cat <(printf 'hello world\n')'
==

The last case above (with "/bin/sh") is what you likely encounter, as "bash" 
when executed as "sh" turns POSIX on
(detailed here: 
http://www.gnu.org/software/bash/manual/html_node/Bash-POSIX-Mode.html#Bash-POSIX-Mode
 ).


Couple of possible work-arounds:

1. Change the first line of your shell scripts from "/bin/sh" to "/bin/bash".
2. Add "set +o posix" to the beginning of your shell script, to disable POSIX.
3. Rewrite the script to be POSIX-complaint by writing the two lists to 
temporary files, then running "diff -n" on the files.

-gordon
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