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

[Ole Tange]

On Fri, Aug 21, 2015 at 10:40 PM, Andreas Bernauer
<address@hidden> wrote:
> 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
:
>> 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

Correct. And since quoting can make a command close to unreadable,
consider using a bash function instead:

    varfilt() {
      vcf=$1
      out=$2
      java -jar $GATK -T VariantFiltration -R
      "$REF_DIR/human_g1k_v37.fasta" -V "$vcf" -window 35 -cluster 3
--filterName
      QD --filterExpression "QD < 2.0" --filterName FS --filterExpression "FS
      30.0" -o "$VCF_OUT/$out"
    }
    export -f varfilt
    parallel varfilt {} '{= s:.*/::; s:\.[^.]+$::; s:\.[^.]+$::;
=}'.filtered.vcf ::: "$VCF_IN"/*.vcf

> 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.

GNU Parallel calls a shell, and it is this shell that interprets the
'<' as redirection.

/Ole