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]$
No comments found
Please Sign in or create a free account to add a new ticket.
With your very own profile, you can contribute to projects, track your activity, watch tickets, receive and update tickets through your email and much more.
Create new ticket
Create your profile
Help contribute to this project by taking a few moments to create your personal profile. Create your profile ยป
lightweight workflows for bioinformatics
john.mccallum (at plantandfood)
MF