Simple template issue
Reported by john.mccallum (at plantandfood) | November 14th, 2012 @ 12:35 AM | in v1.1
[cfljam@pgenome 10.Chrom_1]$ pwd
/data/moa/onion/map/20.USDA_2012/10.Chrom_1 [cfljam@pgenome
10.Chrom_1]$ moa show jobid l.o Chrom_1
postcommand l.o fastaExtract -l contig_names -f
/data/moa/db/onion/80.USDAARS/USOH5Comb_454Isotigs.fasta -t
USDA_mapped_contigs_BXA.fasta
precommand l.o awk '/i/ {print substr($1,2,5)}' BXA_map
> contig_nums
process l.M while read LINE ; do grep $LINE
/data/moa/db/onion/80.USDAARS/USOH5Comb_454Isotigs.fasta | awk
'{print substr($1,2)}' ; done
contig_nameswhile read LINE ; do grep $LINE /data/moa/db/onion/80.USDAARS/USOH5Comb_454Isotigs.fasta | awk '{print substr($1,2)}' ; done
<contig_nums > contig_names
title l.o match up SNP map loci to contigs
[cfljam@pgenome 10.Chrom_1]$ moa run Warning: Removing a stale
lockfile
/data/moa/onion/map/20.USDA_2012/10.Chrom_1/.moa/tmp/moa.02c91j.sh:
line 3: syntax error near unexpected token `(' Error: Exit on
error
[cfljam@pgenome 10.Chrom_1]$
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lightweight workflows for bioinformatics
john.mccallum (at plantandfood)
MF