Re: GNU Parallel Bug Reports java flag being interpreted by bash, and 2+ extension chomping

[Andreas Bernauer]

On 21/08/15 19:55, Cameron Prybol wrote:
> ```
> $ ./s13.variant_calibration.sh <http://s13.variant_calibration.sh>
> /bin/bash: 2.0: No such file or directory
> /bin/bash: 2.0: No such file or directory
> [...]
> ```
> 
> is breaking because of the --filterExpression "QD < 2.0" being
> interpreted as a < file input in this command
> 
> ```
> parallel java -jar $GATK -T VariantFiltration -R
> "$REF_DIR/human_g1k_v37.fasta" -V {} -window 35 -cluster 3 --filterName
> QD --filterExpression "QD < 2.0" --filterName FS --filterExpression "FS
>> 30.0" -o "$VCF_OUT/"'{= s:.*/::; s:\.[^.]+$::; s:\.[^.]+$::;
> =}'.filtered.vcf ::: "$(ls "$VCF_IN"/*.vcf)"
> ```

You have to quote your redirection twice in this case:

$ seq 2 | parallel echo "'QD < 2.0'" {}
QD < 2.0 1
QD < 2.0 2

The first set of quotes is consumed by your shell that calls parallel.
The second set of quotes prevents the called shell (or parallel? I'm not
sure) to interpret the '<' as a redirect.


-Andreas