diff --git a/recipes/verkko/meta.yaml b/recipes/verkko/meta.yaml index e16ea34db298b..3c0d7b8048913 100644 --- a/recipes/verkko/meta.yaml +++ b/recipes/verkko/meta.yaml @@ -1,5 +1,5 @@ {% set name = "verkko" %} -{% set version = "2.2" %} +{% set version = "2.2.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/marbl/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz - sha256: 77a6c8e041bc7dd61f724dcafa6ce6bf1ddc3aed163d17536e9612824293cfba + sha256: 4ab40961352cac22eebfb37606c82bb5a589f9361c36430e7278227e62db3860 patches: - osx_availability.patch # [osx] diff --git a/recipes/verkko/osx_availability.patch b/recipes/verkko/osx_availability.patch index 0386fd5187537..69344ea5b476f 100644 --- a/recipes/verkko/osx_availability.patch +++ b/recipes/verkko/osx_availability.patch @@ -1,43 +1,3 @@ -diff --git a/src/Makefile.boilermake b/src/Makefile.boilermake -index 7e2b929..2dfc3b1 100644 ---- a/src/Makefile.boilermake -+++ b/src/Makefile.boilermake -@@ -160,11 +160,18 @@ endef - define ADD_FILE_COPY_RULE - doall: $${TARGET_DIR}/$2 - ifeq ($3,executable) -+ ifeq ($(suffix $(1)),.sh) - $${TARGET_DIR}/$2: $1 - @mkdir -p $$(dir $${TARGET_DIR}/$2) - cat $1 |sed s/'version=""'/'version="$(VERSION)"'/g > $${TARGET_DIR}/$2 - chmod +x $${TARGET_DIR}/$2 - else -+ $${TARGET_DIR}/$2: $1 -+ @mkdir -p $$(dir $${TARGET_DIR}/$2) -+ cp $1 $${TARGET_DIR}/$2 -+ chmod +x $${TARGET_DIR}/$2 -+ endif -+ else - $${TARGET_DIR}/$2: $1 - @mkdir -p $$(dir $${TARGET_DIR}/$2) - cp -pf $1 $${TARGET_DIR}/$2 -diff --git a/src/Makefile b/src/Makefile -index 67975ff..6a0d332 100644 ---- a/src/Makefile -+++ b/src/Makefile -@@ -127,9 +127,9 @@ define SET_DEFAULT_FLAGS - else - TOOLCHAIN := LLVM - TOOLCHAINV := $$(shell ${CXX} -dumpversion) -- CFLAGS := -pthread -fopenmp -fPIC -std=c17 ${1} -- CXXFLAGS := -pthread -fopenmp -fPIC -std=c++20 ${1} -- LDFLAGS := -pthread -fopenmp ${2} -lm -+ CFLAGS := -DBOOST_NO_CXX98_FUNCTION_BASE -pthread -fopenmp -fPIC -std=c17 ${1} -+ CXXFLAGS := -DBOOST_NO_CXX98_FUNCTION_BASE -pthread -fopenmp -fPIC -std=c++20 ${1} -+ LDFLAGS := -DBOOST_NO_CXX98_FUNCTION_BASE -pthread -fopenmp ${2} -lm - endif - - # Build up our preferred set of flags. diff --git a/src/MBG/makefile b/src/MBG/makefile index 0c0113b..c6fd847 100644 --- a/src/MBG/makefile diff --git a/recipes/verkko/version.patch b/recipes/verkko/version.patch deleted file mode 100644 index 65a9a043a84a7..0000000000000 --- a/recipes/verkko/version.patch +++ /dev/null @@ -1,33 +0,0 @@ -diff --git a/src/Makefile b/src/Makefile -index 5f33ff4..25c2285 100644 ---- a/src/Makefile -+++ b/src/Makefile -@@ -301,7 +301,7 @@ - $${OBJS}: SRC_CFLAGS := $${$${TGT}_CFLAGS} $${SRC_CFLAGS} - $${OBJS}: SRC_CXXFLAGS := $${$${TGT}_CXXFLAGS} $${SRC_CXXFLAGS} - $${OBJS}: SRC_DEFS := $$(addprefix -D,$${$${TGT}_DEFS} $${SRC_DEFS}) -- $${OBJS}: SRC_INCDIRS := $$(addprefix -I,\ -+ $${OBJS}: SRC_INCDIRS := $$(addprefix -iquote,\ - $${$${TGT}_INCDIRS} $${SRC_INCDIRS}) - endif - -@@ -389,7 +389,7 @@ - ALL_TGTS := - DEFS := - DIR_STACK := --INCDIRS := -+INCDIRS := utgcns/libboost - TGT_STACK := - - # Discover our OS and architecture. These were previously used to set -@@ -703,7 +703,7 @@ - - # Perform post-processing on global variables as needed. - DEFS := $(addprefix -D,${DEFS}) --INCDIRS := $(addprefix -I,$(call CANONICAL_PATH,${INCDIRS})) --VERSION := verkko release v2.1 -+INCDIRS := $(addprefix -isystem,$(call CANONICAL_PATH,${INCDIRS})) -+VERSION := bioconda $(PKG_NAME) bioconda $(PKG_VERSION) - - # Define the "all" target (which simply builds all user-defined targets) as the - # default goal.