/usr/bin/abyss-pe is in abyss 2.0.2-2.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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# Run the ABySS assembler.
# Written by Shaun Jackman <sjackman@bcgsc.ca> and
# Anthony Raymond <traymond@bcgsc.ca>.
PATH:=/usr/lib/abyss:${PATH}
# Set pipefail to require that all commands of a pipe must succeed.
SHELL=/bin/bash -o pipefail
# Define this environment variable on Mac OS X to read
# compressed files.
export DYLD_FORCE_FLAT_NAMESPACE=1
# Integrate with Sun Grid Engine (SGE)
ifdef JOB_NAME
name?=$(JOB_NAME)
endif
ifdef SGE_TASK_ID
k?=$(SGE_TASK_ID)
endif
ifdef NSLOTS
ifneq ($(NSLOTS), 1)
np?=$(NSLOTS)
endif
endif
# Integrate with Portable Batch System (PBS)
ifdef PBS_JOBNAME
name?=$(PBS_JOBNAME)
endif
ifdef PBS_ARRAYID
k?=$(PBS_ARRAYID)
endif
ifdef PBS_NODEFILE
NSLOTS=$(shell wc -l <$(PBS_NODEFILE))
ifneq ($(NSLOTS), 1)
np?=$(NSLOTS)
endif
endif
# Integrate with Load Sharing Facility (LSF)
ifdef LSB_JOBNAME
name?=$(LSB_JOBNAME)
endif
ifdef LSB_JOBINDEX
k?=$(LSB_JOBINDEX)
endif
ifdef LSB_DJOB_NUMPROC
ifneq ($(LSB_DJOB_NUMPROC), 1)
np?=$(LSB_DJOB_NUMPROC)
endif
endif
ifdef LSF_BINDIR
mpirun?=$(LSF_BINDIR)/mpirun.lsf
endif
# Integrate with IBM LoadLeveler
ifdef LOADL_JOB_NAME
name?=$(LOADL_JOB_NAME)
endif
ifdef LOADL_STEP_ID
k?=$(LOADL_STEP_ID)
endif
ifdef LOADL_HOSTFILE
NSLOTS=$(shell wc -l <$(LOADL_HOSTFILE))
ifneq ($(NSLOTS), 1)
np?=$(NSLOTS)
endif
endif
# Integrate with SLURM
ifdef SLURM_JOB_NAME
name?=$(SLURM_JOB_NAME)
endif
ifdef SLURM_JOBID
k?=$(SLURM_JOBID)
endif
ifdef SLURM_NTASKS
np?=$(SLURM_NTASKS)
endif
# Determine the path to mpirun
mpirun?=$(shell which mpirun)
ifeq ($(mpirun),)
mpirun=mpirun
endif
# Determine the path to the ABySS executables
path?=$(shell dirname `which $(MAKEFILE_LIST)`)
ifdef path
PATH:=$(path):$(PATH)
endif
ifdef db
# Determine the location of sqlite database
override dbopt:=--db=$(db)
# Track data details for database
library ?= ""
strain ?= ""
species ?= ""
endif
# Programs
MARKDOWN=pandoc
map=$(foreach a,$(2),$(call $(1),$(a)))
deref=$($1)
ifdef lib
in?=$(call map, deref, $(lib))
else
ifdef in
lib?=$(name)
$(lib)?=$(in)
endif
endif
pe?=$(lib)
mp?=$(pe)
# Strip spaces from the file paths
ifdef in
override in:=$(strip $(in))
endif
ifdef se
override se:=$(strip $(se))
endif
# Graph file format
graph?=dot
# g is private. Use graph instead.
override g:=$(graph)
# Number of threads
ifdef PE_HOSTFILE
hostname?=$(shell hostname -f)
j?=$(shell awk '$$1 == "$(hostname)" {print $$2}' $(PE_HOSTFILE))
endif
ifeq ($j,)
j:=$(np)
endif
ifeq ($j,)
j:=2
endif
# ABYSS parameters
q ?= 3
abyssopt += -k$k -q$q
ifdef K
abyssopt += -K$K
endif
ifdef e
abyssopt += -e$e
endif
ifdef E
abyssopt += -E$E
endif
ifdef t
abyssopt += -t$t
endif
ifdef c
abyssopt += -c$c
endif
ifdef b
abyssopt += -b$b
pbopt += -b$b
endif
ifdef Q
abyssopt += -Q$Q
endif
ifdef ss
SS=--SS
endif
abyssopt += $v
# additional params for Bloom filter assembly (`abyss-bloom-dbg`)
ifdef B
abyssopt += -b$B
ifdef H
abyssopt += -H$H
endif
ifdef j
abyssopt += -j$j
endif
ifdef kc
abyssopt += --kc=$(kc)
endif
ifdef x
abyssopt += -s$x
endif
else
abyssopt += $(dbopt) $(SS) --coverage-hist=coverage.hist -s $*-bubbles.fa
endif
# AdjList parameters
m?=50
alopt += $v $(dbopt) $(SS) -k$k -m$m
ifndef B
ifdef K
alopt += -K$K
endif
endif
# filtergraph parameters
ifndef B
ifdef K
fgopt += --assemble --shim-max-degree=2
endif
endif
ifdef xtip
fgopt += -t$(shell echo $k*2 |bc)
endif
# PopBubbles parameters
p?=0.9
pbopt += -p$p
ifdef a
pbopt += -a$a
endif
# Keep sequence and quality strings of read alignments
ifdef ssq
ssq_t :=-ssq
endif
# Aligner parameters
aligner?=map$(ssq_t)
ifeq ($(SS),--SS)
ifneq ($(aligner),map$(ssq_t))
$(warning warning: setting aligner to abyss-map$(ssq_t) since other aligners do not support ss=1)
override aligner=map$(ssq_t)
endif
endif
align?=abyss-$(aligner)
mapopt=$v $(dbopt) -j$j -l$($*_l) $(SS) $(ALIGNER_OPTIONS) $(MAP_OPTIONS)
# DIDA parameters
escape_quotes=$(shell echo "$(1)" | sed 's|"|\\\"|g')
ifeq ($(aligner),dida)
ifdef np
mapopt+=-n$(np)
endif
ifdef DIDA_RUN_OPTIONS
mapopt+=$(DIDA_RUN_OPTIONS)
endif
ifdef DIDA_MPIRUN
mapopt+=-m"$(call escape_quotes,$(DIDA_MPIRUN))"
endif
ifdef DIDA_OPTIONS
mapopt+=-d"$(call escape_quotes,$(DIDA_OPTIONS))"
endif
endif
# fixmate parameters
ifeq ($(align),abyss-kaligner)
fixmate?=ParseAligns
else
fixmate?=abyss-fixmate$(ssq_t)
endif
fmopt=$v $(dbopt) -l$($*_l) $(FIXMATE_OPTIONS)
# DistanceEst parameters
DistanceEst?=DistanceEst$(ssq_t)
l?=40
s?=1000
n?=10
libs=$(pe) $(mp)
$(foreach i,$(libs),$(eval $i_l?=$l))
$(foreach i,$(libs),$(eval $i_s?=$s))
$(foreach i,$(libs),$(eval $i_n?=$n))
deopt=$v $(dbopt) -j$j -k$k -l$($*_l) -s$($*_s) -n$($*_n) $($*_de) \
$(DISTANCEEST_OPTIONS)
scaffold_deopt=--dot --mean $(deopt)
# SimpleGraph parameters
sgopt += $(dbopt)
ifdef d
sgopt += -d$d
endif
# MergePaths parameters
mpopt += $v $(dbopt) -j$j -k$k
# PathOverlap parameters
poopt += $v $(dbopt) -k$k
# PathConsensus parameters
pcopt += $(dbopt)
ifdef a
pcopt += -a$a
endif
pcopt += -p$p
# MergeContigs parameters
mcopt += $v $(dbopt) -k$k
# Scaffold parameters
S?=1000-10000
N?=$n
scopt += $v $(dbopt) $(SS) -k$k
ifdef G
scopt += -G$G
endif
# abyss-fac parameters
ifdef G
override facopt = -G$G
endif
# BWA-SW parameters
bwaswopt=-t$j
BWASW_OPTIONS='-b9 -q16 -r1 -w500'
# Remove environment variables
unexport in se $(lib) $(pe) $(mp) $(long)
# Check the mandatory parameters
ifndef name
error::
@>&2 echo 'abyss-pe: missing parameter `name`'
endif
ifndef k
error::
@>&2 echo 'abyss-pe: missing parameter `k`'
endif
ifeq ($(lib)$(in)$(se),)
error::
@>&2 echo 'abyss-pe: missing parameter `lib`, `in` or `se`'
endif
default:
error::
@>&2 echo 'Try `abyss-pe help` for more information.'
@false
# Help and version messages
help:
@echo 'Usage: abyss-pe [OPTION]... [PARAMETER=VALUE]... [COMMAND]...'
@echo 'Assemble reads into contigs and scaffolds. ABySS is a de novo'
@echo 'sequence assembler intended for short paired-end reads and large'
@echo 'genomes. See the abyss-pe man page for documentation of assembly'
@echo 'parameters and commands. abyss-pe is a Makefile script, and so'
@echo 'options of `make` may also be used with abyss-pe. See the `make`'
@echo 'man page for documentation.'
@echo
@echo 'Report bugs to https://github.com/bcgsc/abyss/issues or abyss-users@bcgsc.ca.'
version:
@echo "abyss-pe (ABySS) 2.0.1"
@echo "Written by Shaun Jackman and Anthony Raymond."
@echo
@echo "Copyright 2012 Canada's Michael Smith Genome Science Centre"
versions: version
@echo PATH=$(PATH)
@ABYSS --version; echo
@-ABYSS-P --version; echo
@AdjList --version; echo
@DistanceEst --version; echo
@MergeContigs --version; echo
@MergePaths --version; echo
@Overlap --version; echo
@PathConsensus --version; echo
@PathOverlap --version; echo
@PopBubbles --version; echo
@SimpleGraph --version; echo
@abyss-fac --version; echo
@abyss-filtergraph --version; echo
@abyss-fixmate --version; echo
@abyss-map --version; echo
@abyss-scaffold --version; echo
@abyss-sealer --version; echo
@abyss-todot --version; echo
@$(align) --version; echo
@awk --version; echo
@sort --version; echo
@-mpirun --version
# Determine the default target
ifdef db
default: startDb
endif
default: unitigs
ifneq ($(in),)
default: contigs contigs-graph
endif
ifneq ($(mp),)
default: scaffolds scaffolds-graph
ifneq ($(long),)
default: long-scaffs long-scaffs-graph
endif
endif
ifdef db
default: finishDb
endif
default: stats
# Define the commands (phony targets)
unitigs: $(name)-unitigs.fa
unitigs-graph: $(name)-unitigs.$g
pe-index: $(name)-3.fa.fm
pe-sam: $(addsuffix -3.sam.gz, $(pe))
pe-bam: $(addsuffix -3.bam.bai, $(pe))
contigs: $(name)-contigs.fa
contigs-graph: $(name)-contigs.$g
mp-index: $(name)-6.fa.fm
mp-sam: $(addsuffix -6.sam.gz, $(mp))
mp-bam: $(addsuffix -6.bam.bai, $(mp))
scaffolds: $(name)-scaffolds.fa
scaffolds-graph: $(name)-scaffolds.$g
seal-scaffolds: $(name)-scaffolds-sealed.fa
scaftigs: $(name)-scaftigs.fa $(name)-scaftigs.agp
long-scaffs: $(name)-long-scaffs.fa
long-scaffs-graph: $(name)-long-scaffs.$g
all: default bam stats
clean:
rm -f *.adj *.asqg *.dot *.gfa *.sam *.txt \
*.sam.gz *.hist *.dist *.path *.path[123]
ifdef db
.PHONY: startDb finishDb
endif
.PHONY: bam default stats \
unitigs unitigs-graph \
pe-index pe-sam pe-bam contigs contigs-graph \
mp-index mp-sam mp-bam scaffolds scaffolds-graph \
scaftigs long-scaffs long-scaffs-graph seal-scaffolds \
all clean help version versions
.DELETE_ON_ERROR:
.SECONDARY:
# Utilities
%.fa.fai: %.fa
abyss-index $v --fai $<
%.fa.fm: %.fa
abyss-index $v $<
%.bam: %.sam.gz
samtools view -Sb $< -o $@
%.bam.bai: %.bam
samtools index $<
# Assemble unitigs
ifdef db
startDb:
@echo -e \
$(name)".sqlite\n"\
> name.txt
@echo -e \
$(shell echo `date +%s`"_"`whoami`_)\
$(shell echo $$RANDOM \% 1000 \+ 1 | bc)"\n"\
$(library)"\n"\
$(strain)"\n"\
$(species)"\n"\
$(name)"\n"\
$(k)"\n"\
$(lib)$(in)$(se)\
> db.txt
endif
ifdef B
%-1.fa:
abyss-bloom-dbg $(abyssopt) $(ABYSS_OPTIONS) $(in) $(se) > $@
else ifdef K
ifdef np
%-1.fa:
$(mpirun) -np $(np) abyss-paired-dbg-mpi $(abyssopt) $(ABYSS_OPTIONS) -o $*-1.fa $(in) $(se)
else
%-1.fa %-1.$g:
abyss-paired-dbg $(abyssopt) $(ABYSS_OPTIONS) -o $*-1.fa -g $*-1.$g $(in) $(se)
endif
else ifdef np
%-1.fa:
$(mpirun) -np $(np) ABYSS-P $(abyssopt) $(ABYSS_OPTIONS) -o $@ $(in) $(se)
else
%-1.fa:
ABYSS $(abyssopt) $(ABYSS_OPTIONS) -o $@ $(in) $(se)
endif
# Find overlapping contigs
%-1.$g: %-1.fa
AdjList $(alopt) --$g $< >$@
# Remove shim contigs
%-2.$g1 %-1.path: %-1.$g %-1.fa
abyss-filtergraph $v --$g $(fgopt) $(FILTERGRAPH_OPTIONS) -k$k -g $*-2.$g1 $^ >$*-1.path
%-2.fa %-2.$g: %-1.fa %-2.$g1 %-1.path
MergeContigs $(mcopt) -g $*-2.$g -o $*-2.fa $^
# Pop bubbles
%-2.path %-3.$g: %-2.fa %-2.$g
PopBubbles $v --$g -j$j -k$k $(SS) $(pbopt) $(POPBUBBLES_OPTIONS) -g $*-3.$g $^ >$*-2.path
%-3.fa: %-2.fa %-2.$g %-2.path
MergeContigs $(mcopt) -o $@ $^
awk '!/^>/ {x[">" $$1]=1; next} {getline s} $$1 in x {print $$0 "\n" s}' \
$*-2.path $*-1.fa >$*-indel.fa
%-unitigs.fa: %-3.fa
ln -sf $< $@
%-unitigs.$g: %-3.$g
ln -sf $< $@
# Estimate distances between unitigs
%-3.sam.gz %-3.hist: $(name)-3.fa
$(align) $(mapopt) $(strip $($*)) $< \
|$(fixmate) $(fmopt) -h $*-3.hist \
|sort -snk3 -k4 \
|gzip >$*-3.sam.gz
%-3.bam %-3.hist: $(name)-3.fa
$(align) $(mapopt) $(strip $($*)) $< \
|$(fixmate) $(fmopt) -h $*-3.hist \
|sort -snk3 -k4 \
|samtools view -Sb - -o $*-3.bam
%-3.dist: %-3.sam.gz %-3.hist
gunzip -c $< \
|$(DistanceEst) $(deopt) -o $@ $*-3.hist
%-3.dist: %-3.bam %-3.hist
samtools view -h $< \
|$(DistanceEst) $(deopt) -o $@ $*-3.hist
%-3.dist: $(name)-3.fa
$(align) $(mapopt) $(strip $($*)) $< \
|$(fixmate) $(fmopt) -h $*-3.hist \
|sort -snk3 -k4 \
|$(DistanceEst) $(deopt) -o $@ $*-3.hist
dist=$(addsuffix -3.dist, $(pe))
ifneq ($(name)-3.dist, $(dist))
$(name)-3.dist: $(name)-3.fa $(dist)
abyss-todot $v --dist -e $^ >$@
$(name)-3.bam: $(addsuffix -3.bam, $(pe))
samtools merge -r $@ $^
endif
# Find overlaps between contigs
%-4.fa %-4.$g: %-3.fa %-3.$g %-3.dist
Overlap $v --$g $(SS) $(OVERLAP_OPTIONS) -k$k -g $*-4.$g -o $*-4.fa $^
# Assemble contigs
%-4.path1: %-4.$g %-3.dist
SimpleGraph $v $(sgopt) $(SIMPLEGRAPH_OPTIONS) -j$j -k$k -o $@ $^
%-4.path2: %-4.path1 %-3.fa.fai %-4.fa.fai
cat $*-3.fa.fai $*-4.fa.fai \
|MergePaths $(mpopt) $(MERGEPATHS_OPTIONS) -o $@ - $<
%-4.path3: %-4.$g %-4.path2
PathOverlap --assemble $(poopt) $(SS) $^ >$@
ifndef cs
%-5.path %-5.fa %-5.$g: %-3.fa %-4.fa %-4.$g %-4.path3
cat $(wordlist 1, 2, $^) \
|PathConsensus $v --$g -k$k $(pcopt) $(PATHCONSENSUS_OPTIONS) -o $*-5.path -s $*-5.fa -g $*-5.$g - $(wordlist 3, 4, $^)
%-6.fa: %-3.fa %-4.fa %-5.fa %-5.$g %-5.path
cat $(wordlist 1, 3, $^) |MergeContigs $(mcopt) -o $@ - $(wordlist 4, 5, $^)
else
%-5.$g %-5.path: %-4.$g %-4.path3
ln -sf $*-4.$g $*-5.$g
ln -sf $*-4.path3 $*-5.path
%-cs.fa: %-3.fa %-4.fa %-4.$g %-4.path3
cat $(wordlist 1, 2, $^) |MergeContigs $(mcopt) -o $@ - $(wordlist 3, 4, $^)
# Convert colour-space sequence to nucleotides
%-6.fa: %-cs.fa
KAligner $v --seq -m -j$j -l$l $(in) $(se) $< \
|Consensus $v -o $@ $<
endif
%-6.$g: %-5.$g %-5.path
PathOverlap --overlap $(poopt) --$g $^ >$@
%-contigs.fa: %-6.fa
ln -sf $< $@
%-contigs.$g: %-6.$g
ln -sf $< $@
# Estimate distances between contigs
%-6.sam.gz %-6.hist: $(name)-6.fa
$(align) $(mapopt) $(strip $($*)) $< \
|$(fixmate) $(fmopt) -h $*-6.hist \
|sort -snk3 -k4 \
|gzip >$*-6.sam.gz
%-6.bam %-6.hist: $(name)-6.fa
$(align) $(mapopt) $(strip $($*)) $< \
|$(fixmate) $(fmopt) -h $*-6.hist \
|sort -snk3 -k4 \
|samtools view -Sb - -o $*-6.bam
%-6.dist.dot: %-6.sam.gz %-6.hist
gunzip -c $< \
|$(DistanceEst) $(scaffold_deopt) -o $@ $*-6.hist
%-6.dist.dot: %-6.bam %-6.hist
samtools view -h $< \
|$(DistanceEst) $(scaffold_deopt) -o $@ $*-6.hist
%-6.dist.dot: $(name)-6.fa
$(align) $(mapopt) $(strip $($*)) $< \
|$(fixmate) $(fmopt) -h $*-6.hist \
|sort -snk3 -k4 \
|$(DistanceEst) $(scaffold_deopt) -o $@ $*-6.hist
# Scaffold
%-6.path: $(name)-6.$g $(addsuffix -6.dist.dot, $(mp))
abyss-scaffold $(scopt) -s$S -n$N -g $@.dot $(SCAFFOLD_OPTIONS) $^ >$@
%-7.path %-7.$g %-7.fa: %-6.fa %-6.$g %-6.path
PathConsensus $v --$g -k$k $(pcopt) $(PATHCONSENSUS_OPTIONS) -s $*-7.fa -g $*-7.$g -o $*-7.path $^
%-8.fa: %-6.fa %-7.fa %-7.$g %-7.path
cat $(wordlist 1, 2, $^) \
|MergeContigs $(mcopt) -o $@ - $(wordlist 3, 4, $^)
%-8.$g: %-7.$g %-7.path
PathOverlap --overlap $(poopt) --$g $^ >$@
%-scaffolds.fa: %-8.fa
ln -sf $< $@
%-scaffolds.$g: %-8.$g
ln -sf $< $@
# Sealed Scaffold
sealer_ks?=-k90 -k80 -k70 -k60 -k50 -k40 -k30
%-8_scaffold.fa: %-8.fa
abyss-sealer -v -j$j --print-flanks -o$*-8 -S$< $(sealer_ks) $(SEALER_OPTIONS) $(in) $(se)
%-scaffolds-sealed.fa: %-8_scaffold.fa
ln -s $< $@
# Scaftig
%-scaftigs.fa: %-scaffolds-agp.fa
ln -sf $< $@
%-scaftigs.agp: %-scaffolds.agp
ln -sf $< $@
# Transcriptome assisted scaffolding
%.fa.bwt: %.fa
bwa index $<
%-8.sam.gz: $(name)-8.fa.bwt
bwa mem -a -t$j -S -P -k$l $(name)-8.fa $(strip $($*)) \
|gzip >$@
%-8.dist.dot: %-8.sam.gz
abyss-longseqdist -k$k $(LONGSEQDIST_OPTIONS) $< \
|grep -v "l=" >$@
%-8.path: $(name)-8.$g $(addsuffix -8.dist.dot, $(long))
abyss-scaffold $(scopt) -s$S -n1 -g $@.$g $(SCAFFOLD_OPTIONS) $^ >$@
%-9.path %-9.$g %-9.fa: %-8.fa %-8.$g %-8.path
PathConsensus $v --$g -k$k $(pcopt) $(PATHCONSENSUS_OPTIONS) -s $*-9.fa -g $*-9.$g -o $*-9.path $^
%-10.fa: %-8.fa %-9.fa %-9.$g %-9.path
cat $(wordlist 1, 2, $^) \
|MergeContigs $(mcopt) -o $@ - $(wordlist 3, 4, $^)
%-10.$g: %-9.$g %-9.path
PathOverlap --overlap $(poopt) --$g $^ >$@
%-long-scaffs.fa: %-10.fa
ln -sf $< $@
%-long-scaffs.$g: %-10.$g
ln -sf $< $@
ifdef db
finishDb:
@rm -f db.txt
endif
# Create the final BAM file
ifneq ($(mp),)
bam: $(name)-scaffolds.bam.bai
else
ifneq ($(in),)
bam: $(name)-contigs.bam.bai
else
bam: $(name)-unitigs.bam.bai
endif
endif
$(name)-unitigs.bam: %.bam: %.fa
$(align) $v -j$j -l$l $(ALIGNER_OPTIONS) $(se) $< \
|samtools view -Su - |samtools sort -o - - >$@
$(name)-contigs.bam $(name)-scaffolds.bam: %.bam: %.fa
$(align) $v -j$j -l$l $(ALIGNER_OPTIONS) \
$(call map, deref, $(sort $(lib) $(pe) $(mp))) $< \
|$(fixmate) $v $(FIXMATE_OPTIONS) \
|sort -snk3 -k4 \
|samtools view -Sb - >$@
# Align the variants to the assembly
%-variants.bam: %.fa.bwt
bwa bwasw -t$j $*.fa <(cat $(name)-bubbles.fa $(name)-indel.fa) \
|samtools view -Su - |samtools sort -o - - >$@
%-variants.vcf.gz: %.fa %-variants.bam
samtools mpileup -Buf $^ |bcftools view -vp1 - |bgzip >$@
%.gz.tbi: %.gz
tabix -pvcf $<
# Calculate assembly contiguity statistics
stats: $(name)-stats.tab $(name)-stats $(name)-stats.csv $(name)-stats.md
ifneq ($(shell which $(MARKDOWN) 2>/dev/null),)
stats: $(name)-stats.html
endif
%-stats: %-stats.tab
ln -sf $< $@
$(name)-stats.tab: %-stats.tab: %-unitigs.fa
ifneq ($(in),)
$(name)-stats.tab: %-stats.tab: %-contigs.fa
endif
ifneq ($(mp),)
$(name)-stats.tab: %-stats.tab: %-scaffolds.fa
endif
ifneq ($(long),)
$(name)-stats.tab: %-stats.tab: %-long-scaffs.fa
endif
$(name)-stats.tab:
abyss-fac $(facopt) $(FAC_OPTIONS) $^ |tee $@
%.csv: %.tab
tr '\t' , <$< >$@
%.md: %.tab
abyss-tabtomd $< >$@
%.html: %.md
$(MARKDOWN) $< >$@
# Create an AGP file and FASTA file of scaftigs from scaffolds
%.agp %-agp.fa: %.fa
abyss-fatoagp $(FATOAGP_OPTIONS) -f $*-agp.fa $< >$*.agp
# Align the contigs to the reference
%-$(ref).sam.gz: %.fa
bwa bwasw $(bwaswopt) $(BWASW_OPTIONS) $($(ref)) $< |gzip >$@
# Find breakpoints in the alignments
%.break: %.sam.gz
abyss-samtobreak $(SAMTOBREAK_OPTIONS) $< >$@
# Report ABySS configuration variable(s) and value(s) currently set.
override varList := a b c d e E G j k l m n N p q s S t v cs pi \
np pe lib mp se SS hostname xtip \
ssq ssq_ti libs path name in mpirun \
aligner long ref fixmate DistanceEst \
map deref abyssopt fgopt pbopt \
align mapopt fmopt deopt \
pcopt sgopt bwaswopt \
ABYSS_OPTIONS FILTERGRAPH_OPTIONS POPBUBBLES_OPTIONS \
OVERLAP_OPTIONS SIMPLEGRAPH_OPTIONS MERGEPATHS_OPTIONS \
SCAFFOLD_OPTIONS ALIGNER_OPTIONS MAP_OPTIONS FAC_OPTIONS \
FIXMATE_OPTIONS BWASW_OPTIONS FATOAGP_OPTIONS SAMTOBREAK_OPTIONS \
MARKDOWN
env:
@echo 'List of ABySS configuration variables currently set:'
@echo '[environment], if variable was inherited from the environment.'
@echo '[command line], if variable was defined on the command line.'
@echo '[file], if variable was defined in (this) makefile.'
@echo '[override], if variable was defined with an override directive in (this) makefile.'
@$(foreach var,$(varList),\
echo -e $(var)" = "$($(var))"\t["$(origin $(var))"]" | grep -v "undefined";)
|