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update to verkko v2.2.1 #51111

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Oct 3, 2024
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7 changes: 6 additions & 1 deletion recipes/verkko/build.sh
Original file line number Diff line number Diff line change
@@ -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

Expand All @@ -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 [ "$(uname)" == "Darwin" ]; then
Expand All @@ -18,6 +24,5 @@ fi
make clean && make -j$CPU_COUNT
popd

mkdir -p "$PREFIX/bin"
cp -rf bin/* $PREFIX/bin/
cp -rf lib/* $PREFIX/lib/
21 changes: 10 additions & 11 deletions recipes/verkko/meta.yaml
Original file line number Diff line number Diff line change
@@ -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
Expand All @@ -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
Expand All @@ -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:
Expand Down
40 changes: 0 additions & 40 deletions recipes/verkko/osx_availability.patch
Original file line number Diff line number Diff line change
@@ -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
Expand Down
33 changes: 0 additions & 33 deletions recipes/verkko/version.patch

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