#!/opt/gensoft/exe/amos/3.1.0/bin/runAmos -C
# `minimus' - The AMOS Lightweight Assembler Pipeline

#--------------------------------------- USER DEFINED VALUES ------------------#
TGT = $(strip .frg PREFIX).afg
#------------------------------------------------------------------------------#
PREF = $(strip .frg PREFIX)


BANK    = $(PREF).bnk
CONTIG  = $(PREF).contig
FASTA   = $(PREF).fasta

## Converting to AFG
10: toAmos -f $(PREFIX) -o $(TGT)

## Building AMOS bank
20: bank-transact -c -z -b $(BANK) -m $(TGT)

## Assembling fragments
30: preassembleFrgs $(BANK)

## Outputting contigs
40: bank2contig $(BANK) > $(CONTIG)

## Converting to FastA file
50: bank2fasta -b $(BANK) > $(FASTA)
