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Re: GNU Parallel Bug Reports java flag being interpreted by bash, and 2+
From: |
Andreas Bernauer |
Subject: |
Re: GNU Parallel Bug Reports java flag being interpreted by bash, and 2+ extension chomping |
Date: |
Fri, 21 Aug 2015 22:46:35 +0200 |
User-agent: |
Mozilla/5.0 (Macintosh; Intel Mac OS X 10.10; rv:38.0) Gecko/20100101 Thunderbird/38.2.0 |
On 21/08/15 19:55, Cameron Prybol wrote:
> an additional problem I have is with the tandem extension dropping
>
> for example
> ```
> parallel java -jar \
> $GATK \
> -T HaplotypeCaller \
> -R "$REF_DIR/human_g1k_v37.fasta" \
> -I {} \
> -dontUseSoftClippedBases \
> --dbsnp "$REF_DIR/dbsnp_138.b37.vcf" \
> -stand_call_conf 20 \
> -stand_emit_conf 20 \
> -o "$VCF_OUT/"'{= s:.*/::; s:\.[^.]+$::; s:\.[^.]+$::; =}'.vcf \
> ::: "$(ls "$BAM_DIR"/*.score_recalibrated.bam)"
> ```
>
> runs fine with the perl regular expressions in tandem, but anytime I
> want to drop two or more extensions i.e. {/..}, {/...} it fails
>
> ```
> parallel java -jar \
> $GATK \
> -T HaplotypeCaller \
> -R "$REF_DIR/human_g1k_v37.fasta" \
> -I {} \
> -dontUseSoftClippedBases \
> --dbsnp "$REF_DIR/dbsnp_138.b37.vcf" \
> -stand_call_conf 20 \
> -stand_emit_conf 20 \
> -o "$VCF_OUT/"'{/..}'.vcf \
> ::: "$(ls "$BAM_DIR"/*.score_recalibrated.bam)"
> ```
I think you have to activate '{/..}' with --plus:
$ echo 'a/b/c/test.1.2' | parallel --plus echo {/..}
test
{= ... =} and {/.} are built-in, though.
-Andreas