Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
branch: master
Fetching contributors…

Cannot retrieve contributors at this time

57 lines (43 sloc) 1.601 kb
SCAFFOLD=assembly/scaffold.yml
SEQUENCE=assembly/sequence.fna
ANNTTION=assembly/annotations.gff
TEMPLATE=submission/template.sbt
TABLE=plasmid.tbl
GENOME=plasmid.fsa
GENOMESQN=plasmid.sqn
GENOMEGBF=plasmid.gbf
GENOMEMAP=plasmid.map
LOG=plasmid.val
all: $(AGP) $(GENOMESQN) $(LOG) $(GENOMEMAP)
$(LOG): $(GENOME) $(TABLE) $(TEMPLATE)
tbl2asn -p . -M n -t $(TEMPLATE) -Z $@
rm -f errorsummary.val
$(GENOMEGBF): $(GENOME) $(TABLE) $(TEMPLATE)
tbl2asn -p . -V b -t $(TEMPLATE)
$(GENOMESQN): $(GENOME) $(TABLE) $(TEMPLATE)
tbl2asn -p . -t $(TEMPLATE) -i $(GENOME) -c b
$(GENOMEMAP): $(SCAFFOLD) $(SEQUENCE) $(ANNTTION)
genomer view mapping \
--reset_locus_numbering \
--prefix='E1A_' \
> $@
$(GENOME): $(SCAFFOLD) $(SEQUENCE)
genomer view fasta \
--identifier='PRJNA46289' \
--organism='Pseudomonas fluorescens' \
--strain='R124' \
--gcode='11' \
--topology='circular' \
--isolation-source='Orthoquartzite Cave Surface' \
--collection-date='17-Oct-2007' \
--completeness='Complete' \
> $@
$(TABLE): $(SCAFFOLD) $(SEQUENCE) $(ANNTTION)
genomer view table \
--identifier=PRJNA46289 \
--reset_locus_numbering \
--prefix='E1A_' \
--generate_encoded_features='gnl|BartonUAkron|' \
> $@
clean:
rm -f plasmid.*
Jump to Line
Something went wrong with that request. Please try again.