Redirect stdout to a file with bash command in brackets

Question

I have a bash command built from an array as following:

cmd=(java -Xmx8g -jar program.jar input.vcf ">" output.vcf)

I do not have problems when using echo:

echo "${cmd[@]}" java -Xmx8g -jar program.jar input.vcf > output.vcf

But when I run it using:

"${cmd[@]}"

The > is ignored and I cannot redirect stdout to output.vcf file.

Please, could you suggest me a solution?

When you pass it that way, the > isn't ignored; instead, it's passed to the Java program as an argument. — Charles Duffy
– Charles Duffy, Commented Sep 19, 2014 at 23:47
That's a (security and correctness) feature, not a bug -- it means that data (like arguments) can't be treated as code without intentional action to the contrary. — Charles Duffy
– Charles Duffy, Commented Sep 19, 2014 at 23:48
@ooga, ...thereby completely bypassing said security, and also losing any advantage from using proper array expansion syntax. — Charles Duffy
– Charles Duffy, Commented Sep 19, 2014 at 23:49
BTW, the answer provided by @JohnKugelman is echoed as a best practice by BashFAQ #50: mywiki.wooledge.org/BashFAQ/050 — Charles Duffy
– Charles Duffy, Commented Sep 19, 2014 at 23:52

John Kugelman · Accepted Answer · 2014-09-19 23:46:07Z

It would be better to store the command in a function. Functions are for commands, variables are for data.

cmd() { java -Xmx8g -jar program.jar input.vcf > output.vcf } cmd

(I implore you not to use eval, which allow your variable-based approach to work, but opens up a whole other can of worms.)

5gon12eder · Accepted Answer · 2014-09-19 23:57:17Z

I would prefer John Kugelman's answer but if you really mean to execute the words stored in the array, you could eval them:

cmd=(date '>' date.stdout) eval "${cmd[@]}"

Be warned that this might open up all kinds of security holes.

2 Answers 2