Update cactus to 3.1.4

recipes/cactus/build.sh

@@ -13,6 +13,17 @@ make EXTRA_FLAGS="-O3 -Wall -Wno-unused-function -Wno-misleading-indentation -DU
 cd ../../
 
 cd submodules/FASTGA
+make CFLAGS="${CFLAGS} -Wno-implicit-function-declaration -O3 -L${PREFIX}/lib" CC="${CC}" -j"${CPU_COUNT}"
+cd ../../
+
+cd submodules/FASTAN
+sed -i.bak -e 's/-lm -lz/-lm -lpthread -lz/g' Makefile
+rm -f *.bak
+make CFLAGS="${CFLAGS} -Wno-implicit-function-declaration -O3 -L${PREFIX}/lib" CC="${CC}" -j"${CPU_COUNT}" FasTAN
+ln -f FasTAN "${PREFIX}/bin/"
+cd ../../
+
+cd submodules/alntools
 make CFLAGS="${CFLAGS} -O3 -L${PREFIX}/lib" CC="${CC}" -j"${CPU_COUNT}"
 cd ../../
 
@@ -23,7 +34,7 @@ cd ../../../../../
 
 sed -i.bak 's|find_packages|find_namespace_packages|' setup.py
 rm -rf *.bak
-${PYTHON} -m pip install . --no-deps --no-build-isolation --no-cache-dir --use-pep517 -vvv
+${PYTHON} -m pip install ./submodules/sonLib . --no-deps --no-build-isolation --no-cache-dir --use-pep517 -vvv
 
 make
 mv bin/* ${PREFIX}/bin

recipes/cactus/makefile.patch

@@ -1,24 +1,34 @@
 diff --git a/Makefile b/Makefile
-index 1934e97c..183bf9fc 100644
+index 9fabeb0a..9024dc94 100644
 --- a/Makefile
 +++ b/Makefile
-@@ -6,7 +6,7 @@ modules = api setup caf bar hal reference pipeline preprocessor
-
+@@ -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
--submodules1 = sonLib cPecan hal matchingAndOrdering pinchesAndCacti abPOA lastz paffy red collapse-bubble FASTGA
-+submodules1 = sonLib cPecan hal matchingAndOrdering pinchesAndCacti abPOA paffy red collapse-bubble FASTGA
+ # 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 paffy red collapse-bubble FASTGA alntools
  submodules2 = cactus2hal
  submodules = ${submodules1} ${submodules2}
 
-@@ -259,10 +259,6 @@ suball.abPOA:
+@@ -294,11 +294,6 @@ suball.abPOA:
  	ln -f submodules/abPOA/include/*.h ${INCLDIR}
  	rm -fr ${INCLDIR}/simde && cp -r submodules/abPOA/include/simde ${INCLDIR}
 
 -suball.lastz:
--	cd submodules/lastz && ${MAKE}
+-	cd submodules/lastz/src && sed -i Makefile -e 's/-lm -o/-lm $${LIBS} -o/g'
+-	cd submodules/lastz && LIBS="${jemallocLib}" ${MAKE}
 -	ln -f submodules/lastz/src/lastz bin
 -
  suball.paffy:
- 	cd submodules/paffy && ${MAKE}
+ 	cd submodules/paffy && LIBS="${jemallocLib}" ${MAKE}
  	rm -rf submodules/paffy/bin/*.dSYM
+
+@@ -321,7 +321,4 @@
+	ln -f submodules/FASTGA/GIXmake ${BINDIR}
+	ln -f submodules/FASTGA/GIXrm ${BINDIR}
+-suball.FASTAN:
+-	cd submodules/FASTAN && sed -i Makefile -e 's/-lm -lz/-lm -lpthread -lz/g' && ${MAKE} || true
+- 	ln -f submodules/FASTAN/FasTAN ${BINDIR}
+ suball.alntools:
+	cd submodules/alntools && ${MAKE}

recipes/cactus/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "cactus" %}
-{% set version = "3.0.1" %}
+{% set version = "3.1.4" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
   url: https://github.com/ComparativeGenomicsToolkit/cactus/releases/download/v{{ version }}/cactus-v{{ version }}.tar.gz
-  sha256: daf3abb6b35116a8d0796247420051d01b92c1c398f38a4116e686f4284a21d7
+  sha256: 11b33e9754f2bdc420f0f6ca76520246f209933636720099864c4b2b894da08c
   patches:
     - include.mk.patch
     - makefile.patch
@@ -41,6 +41,9 @@ requirements:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
     - make
+    - autoconf
+    - automake
+    - libtool
     - pkg-config
     - llvm-openmp  # [osx]
     - libgomp      # [linux]
@@ -57,6 +60,7 @@ requirements:
     - cigar
     - biopython
     - pysam
+    - jemalloc
     - toil  # [x86_64]
     - backports.zoneinfo  # [py39]
   run:
@@ -69,6 +73,7 @@ requirements:
     - cigar
     - biopython
     - pysam
+    - jemalloc
     - toil  # [x86_64]
     - backports.zoneinfo  # [py39]
     - samtools