Hi Assaf, all,
Thanks for the help, I was setting my environment with sh instead of bash, and
calling from bash... I'm not sure I would have ever figured that one out on my
own.
Many, many thanks!!
-Carrie
________________________________________
From: Assaf Gordon [gor...@cshl.edu]
Sent: Wednesday, March 27, 2013 1:56 PM
To: Ganote, Carrie L
Cc: galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Tool run on cluster returns error state on clean
install
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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