syntax error near unexpected token `('
I got the error message when I used command like:
program <(zcat myfile1.gz)<(zcat myfile2.gz)
in a bash script. It works well in my terminal, but when I submit the script to cluster and it always return the error message.
Finally I got the key from Mitch's blog:
http://www.linuxjournal.com/content/shell-process-redirection
It's called process substitution for piping the stdout of multiple commands. Process substitution is not a POSIX compliant feature and so it may have to be enabled via:
set +o posix
After I set the POSIX, it works well! It seems that POSIX is not enabled on the node where the job was submitted.
My learning notes for R, Unix, Perl, statistics, tools/resources, biology etc. everything about Bioinformatics
Showing posts with label pipe. Show all posts
Showing posts with label pipe. Show all posts
Monday, December 09, 2013
Tuesday, May 08, 2012
Super duper command: find
- Find files with filename containing WORD
find -type f -name \*WORDS\* - Find files by name in case-sensitive way, e.g. containing word or Word...
find -type f -iname \*word\* - Find files with name containing "word", "Word" etc., but not "WORD"
find -type f -iname \*word\* -not -name \*WORD\* - Unzip all *.tar.gz files
find -type f -name \*.gz -exec tar -zxvf {} \; - Use pipe in find command
find ~/scratch/RNAseq/ -type f -name clean.fa -printf "a=\`echo %p | cut -f6- -d'/' | sed 's/\//./g'\`; cp %p \$a \n" | sh
# copy /home/dongx/scratch/RNAseq/****/xxxx/clean.fa to ****.xxxx.clean.fa
- http://www.linux.ie/newusers/beginners-linux-guide/find.php
- http://stackoverflow.com/questions/307015/how-do-i-include-a-pipe-in-my-linux-find-exec-command
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