seem to have issues editing command when prefixed by ./
[cfljam@pgenome 09.submission_SSR_reads_sequin]$ pwd
/data/moa/onion/20.genomic.sequencing/09.submission_SSR_reads_sequin
[cfljam@pgenome 09.submission_SSR_reads_sequin]$ moa show input o
/
mode o simple
name_sed o s/a/a/
output_dir o .
postcommand o (undefined)
precommand L awk '!/#/'
../08.submission_SSR_reads/DH2122_skim_seq.fasta.gff | while read
name type what start stop rest; do echo ">Feature" $name; echo
$start $stop "repeat_region rpt_type tandem";
echo $start $stop "repeat_region satellite microsatellite" ; done > SSR_reads.tbl
process L linux.tbl2asn -i
../08.submission_SSR_reads/SSR_marker_reads.fasta -t
template_file.sbt -a s -y "singletons from assembly of genomic skim
sequence" -j "[organism=Allium
cepa][genotype=CUDH2122]" -V vb -Z discreps -o SSR_reads.sqn -f SSR_reads.tbl
project o (undefined)
title L format SSR reads for submission to Genbank
touch o T
[cfljam@pgenome 09.submission_SSR_reads_sequin]$ moa set process
process:
./linux.tbl2asn -i
../08.submission_SSR_reads/SSR_marker_reads.fasta -t
template_file.sbt -a s -y "singletons from assembly of genomic skim
sequence" -j "[organism=Allium cepa][genotype=CUDH2122]" -V vb -Z
discreps -o SSR_reads.sqn -f SSR_reads.tbl [cfljam@pgenome
09.submission_SSR_reads_sequin]$ moa show input o /
mode o simple
name_sed o s/a/a/
output_dir o .
postcommand o (undefined)
precommand L awk '!/#/'
../08.submission_SSR_reads/DH2122_skim_seq.fasta.gff | while read
name type what start stop rest; do echo ">Feature" $name; echo
$start $stop "repeat_region rpt_type tandem";
echo $start $stop "repeat_region satellite microsatellite" ; done > SSR_reads.tbl
process L linux.tbl2asn -i
../08.submission_SSR_reads/SSR_marker_reads.fasta -t
template_file.sbt -a s -y "singletons from assembly of genomic skim
sequence" -j "[organism=Allium
cepa][genotype=CUDH2122]" -V vb -Z discreps -o SSR_reads.sqn -f SSR_reads.tbl
project o (undefined)
title L format SSR reads for submission to Genbank
touch o T
[cfljam@pgenome 09.submission_SSR_reads_sequin]$
