update to verkko v2.2.1 (#51111)

* update to verkko v2.2.1 * clean up recipe * restore build.sh changes: * use explicit rust version * add darwin block back to build.sh --------- Co-authored-by: mencian <joshua.zhuang@yahoo.com>
bioconda · Oct 3, 2024 · 0292cdf · 0292cdf
1 parent 0b873e3
commit 0292cdf
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diff --git a/recipes/verkko/build.sh b/recipes/verkko/build.sh
@@ -1,6 +1,8 @@
 #!/bin/bash
 set -ex
 
+mkdir -p "$PREFIX/bin"
+
 # taken from yacrd recipe, see: https://github.com/bioconda/bioconda-recipes/blob/2b02c3db6400499d910bc5f297d23cb20c9db4f8/recipes/yacrd/build.sh
 if [ "$(uname)" == "Darwin" ]; then
 
@@ -10,6 +12,10 @@ if [ "$(uname)" == "Darwin" ]; then
     mkdir -p $HOME/.cargo/registry/index/
 fi
 
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CFLAGS="${CFLAGS} -O3"
+export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include"
+
 # on osx we remove the built-in boost and make sure todepend on the system boost
 pushd src
 if [ "$(uname)" == "Darwin" ]; then
@@ -18,6 +24,5 @@ fi
 make clean && make -j$CPU_COUNT
 popd
 
-mkdir -p "$PREFIX/bin"
 cp -rf bin/* $PREFIX/bin/
 cp -rf lib/* $PREFIX/lib/
diff --git a/recipes/verkko/meta.yaml b/recipes/verkko/meta.yaml
@@ -1,16 +1,15 @@
 {% set name = "verkko" %}
-{% set version = "2.2" %}
+{% set version = "2.2.1" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 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]
+    - osx_availability.patch  # [osx]
 
 build:
   number: 0
@@ -20,20 +19,20 @@ build:
 requirements:
   build:
     - make
-    - llvm-openmp  # [osx]
-    - libgomp      # [linux]
-    - htslib
     - {{ compiler('cxx') }}
     - rust >=1.74
   host:
-    - boost-cpp >=1.56 #[osx]
+    - boost-cpp >=1.56  #[osx]
     - llvm-openmp  # [osx]
-    - libgomp      # [linux]
+    - libgomp  # [linux]
     - gsl
     - zlib
     - htslib
   run:
     - python >=3.9
+    - boost-cpp >=1.56  #[osx]
+    - llvm-openmp  # [osx]
+    - libgomp  # [linux]
     - pulp <=2.7.0
     - perl >=5.6
     - seqtk
@@ -57,12 +56,12 @@ test:
     - verkko --version
 
 about:
-  home: https://github.com/marbl/verkko
+  home: "https://github.com/marbl/verkko"
   license: CC0
   license_file: README.licenses
   summary: "A hybrid genome assembly pipeline developed for telomere-to-telomere assembly of accurate (HiFi, ONT Duplex, ONT HERRO) and long (ONT UL) reads."
   dev_url: "https://github.com/marbl/verkko"
-  doc_url: "https://github.com/marbl/verkko/blob/master/README.md"
+  doc_url: "https://github.com/marbl/verkko/blob/v{{ version }}/README.md"
 
 extra:
   identifiers:

diff --git 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