Build LAST from a submodule

.gitmodules

@@ -50,3 +50,6 @@
 	path = submodules/minipoa
 	url = https://github.com/ComparativeGenomicsToolkit/minipoa.git
 	branch = cactus-integration
+[submodule "submodules/last"]
+	path = submodules/last
+	url = https://gitlab.com/mcfrith/last.git

Makefile

@@ -7,7 +7,7 @@ modules = api setup caf bar hal reference pipeline preprocessor
 # submodules are in multiple pass to handle dependencies cactus2hal being dependent on
 # both cactus and sonLib
 # jemalloc is conditionally added based on include.mk settings
-submodules1 = sonLib cPecan hal matchingAndOrdering pinchesAndCacti abPOA lastz paffy red collapse-bubble FASTGA FASTAN alntools
+submodules1 = sonLib cPecan hal matchingAndOrdering pinchesAndCacti abPOA lastz last paffy red collapse-bubble FASTGA FASTAN alntools
 ifeq ($(minipoa),on)
 submodules1 += minipoa
 endif
@@ -406,6 +406,24 @@ else
 endif
 	ln -f submodules/lastz/src/lastz bin
 
+# LAST: cactus trains its scoring models with last-train (and lastdb and lastal).  Its makefile writes
+# "CXXFLAGS = ..." with spaces around the '=': make that line add to ours, rather than replace them, and leave the
+# sub-make override on its line 3 alone, since that is how src/makefile receives the value.  Checked, as a sed that
+# stops matching after an upstream change is silently a no-op.  LAST has no LIBS variable either, so add one after
+# the objects: a static archive named before them resolves nothing, and lastal would quietly keep glibc's
+# allocator.  Its -msse4 only suits x86 compilers, and its README has ARM builds go without it too.
+ifdef arm
+lastSedArm = -e 's/ -msse4//'
+endif
+suball.last: suball.jemalloc
+	cd submodules/last && sed -i -e 's/^CXXFLAGS *= */CXXFLAGS += /' ${lastSedArm} makefile && grep -qE '^CXXFLAGS \+= ' makefile \
+	  || { echo "last: no 'CXXFLAGS =' line in its makefile; check that cactus's CXXFLAGS still reach lastal" >&2; exit 1; }
+	cd submodules/last && sed -i -e '/LIBS/!s/ -lz$$/ -lz $$(LIBS)/' src/makefile && grep -q -- '-lz $$(LIBS)' src/makefile \
+	  || { echo "last: no '-lz' link line in src/makefile; check that jemalloc still reaches lastal" >&2; exit 1; }
+	cd submodules/last && CXXFLAGS="$${CXXFLAGS} ${CACTUS_ARCH_FLAGS}" LIBS="${jemallocSubLibs}" ${MAKE}
+	ln -f submodules/last/bin/lastal submodules/last/bin/lastdb submodules/last/bin/last-train \
+	  submodules/last/bin/last-postmask ${BINDIR}
+
 suball.paffy:
 	# paffy carries its own sonLib clone, which is put at the commit cactus pins. That clone has only
 	# fetched what its own pin needed, so bring the commit over from cactus's checkout first.

build-tools/downloadPangenomeTools

@@ -49,7 +49,7 @@ fi
 
 # CPU baseline.  include.mk is the single source of truth; ask make for it rather than
 # duplicating the arm/legacy/x86 selection here, where it would silently drift.  Without this
-# nothing built by this script -- minigraph, minimap2, gfatools, last, samtools/bcftools --
+# nothing built by this script -- minigraph, minimap2, gfatools, samtools/bcftools --
 # gets an arch flag at all: confirmed against the v3.3.0 tarball, where minigraph carried zero
 # AVX2 in its own code, only glibc's runtime-dispatched string routines.
 # MAKEFLAGS is cleared because "make binRelease" reaches this from inside a make recipe.
@@ -427,54 +427,6 @@ then
     mkdir -p ${pangenomeBuildDir}
 fi
 
-# last
-cd ${pangenomeBuildDir}
-git clone https://gitlab.com/mcfrith/last.git --recursive
-cd last
-git checkout 1651
-# last writes "CXXFLAGS = ..." with spaces around the '=', so the old
-# 's/CXXFLAGS=/CXXFLAGS+=/' never matched line 1.  What it did match was the sub-make
-# override on line 3 ($(MAKE) CXXFLAGS="$(CXXFLAGS)" -> CXXFLAGS+="$(CXXFLAGS)"), which only
-# doubled last's own flags while its line-1 assignment carried on clobbering ours -- so
-# nothing cactus sets has ever reached lastal/lastdb.  Anchor to the line start and allow the
-# spaces; leave line 3 alone, since that override is how src/makefile receives the value.
-# Guarded: this sed was silently a no-op for years, which is exactly what we don't want twice.
-grep -qE '^CXXFLAGS *=' makefile || {
-    echo "ERROR: last: no 'CXXFLAGS =' assignment at the start of a line in makefile." >&2
-    echo "       Upstream changed its build; re-check that cactus's CXXFLAGS reach lastal." >&2
-    exit 1
-}
-sed -i makefile -e 's/^CXXFLAGS *= */CXXFLAGS += /'
-# last has no LIBS variable, so add one after the objects.  Order matters: a static archive
-# named before the objects resolves nothing and is discarded, and lastal would silently fall
-# back to glibc's allocator.
-sed -i src/makefile -e '/LIBS/!s/ -lz$/ -lz $(LIBS)/'
-LIBS="${jemallocLib}" make -j ${numcpu}
-if [[ $STATIC_CHECK -ne 1 || $(ldd bin/lastal | grep so | wc -l) -eq 0 ]]
-then
-    mv bin/lastal ${binDir}
-else
-    exit 1
-fi
-if [[ $STATIC_CHECK -ne 1 || $(ldd bin/lastdb | grep so | wc -l) -eq 0 ]]
-then
-    mv bin/lastdb ${binDir}
-else
-    exit 1
-fi
-if [[ $STATIC_CHECK -ne 1 || $(ldd bin/last-train | grep so | wc -l) -eq 0 ]]
-then
-    mv bin/last-train ${binDir}
-else
-    exit 1
-fi
-if [[ $STATIC_CHECK -ne 1 || $(ldd bin/last-postmask | grep so | wc -l) -eq 0 ]]
-then
-    mv bin/last-postmask ${binDir}
-else
-    exit 1
-fi
-
 cd ${CWD}
 rm -rf ${pangenomeBuildDir}