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ghostx: add aarch64/arm64 builds #52967

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merged 7 commits into from
Dec 23, 2024
Merged

ghostx: add aarch64/arm64 builds #52967

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b6a6463
ghostx: add aarch64/arm64 builds
martin-g Dec 23, 2024
f3f7a39
ghostx: Patch the Makefile to be able to use custom CC and CXX
martin-g Dec 23, 2024
c09cb95
Add '-D_LIBCPP_DISABLE_AVAILABILITY' for OSX
martin-g Dec 23, 2024
7ad9b36
Add libgomp/llvm-openmp as host deps
martin-g Dec 23, 2024
af1eef1
Set C++ standard to 14
martin-g Dec 23, 2024
589e7c7
Try without libgomp/llvm-openmp
martin-g Dec 23, 2024
acc7cf6
Re-add libgomp/llvm-openmp
martin-g Dec 23, 2024
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1 change: 0 additions & 1 deletion build-fail-blacklist
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Original file line number Diff line number Diff line change
Expand Up @@ -607,7 +607,6 @@ recipes/fastuniq
recipes/fgap
recipes/funcannot
recipes/genepender
recipes/ghostx
recipes/ls-gkm
recipes/mosaik
recipes/ngmerge
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10 changes: 7 additions & 3 deletions recipes/ghostx/build.sh
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@@ -1,6 +1,10 @@
#!/usr/bin/env bash

set -xe

cd ./src/

make
mkdir -p $PREFIX/bin
CC="${CC}" CXX="${CXX}" CC_FLAGS="${CFLAGS}" make -j"${CPU_COUNT}"

cp ghostx $PREFIX/bin
mkdir -p $PREFIX/bin
install -m 755 ghostx $PREFIX/bin
39 changes: 39 additions & 0 deletions recipes/ghostx/ghostx-makefile.patch
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@@ -0,0 +1,39 @@
diff --git i/src/Makefile w/src/Makefile
index 8844e0a..3248657 100644
--- i/src/Makefile
+++ w/src/Makefile
@@ -1,9 +1,9 @@
LAST_CC=g++
-CC=gcc
-CXX=g++
+CC?=gcc
+CXX?=g++
COMMON_FLAGS=-Wall -Wextra -pedantic -fopenmp -O3
INCLUDES = -I ../ext/boost
-CC_FLAGS=${COMMON_FLAGS}
+CC_FLAGS?=${COMMON_FLAGS}
LDLIBS =-lm -fopenmp

ifeq ($(PROFILE), Yes)
@@ -69,18 +69,18 @@ OBJS += $(CPP_SRC:%.cpp=%.o)
all:ghostx

ghostx: $(OBJS)
- $(LAST_CC) -o $@ $(OBJS) $(LDFLAGS) $(LDLIBS)
+ $(CXX) -std=c++14 -o $@ $(OBJS) $(LDFLAGS) $(LDLIBS)

.c.o:
$(CC) -c $(CC_FLAGS) $< -o $@ $(INCLUDES)

.cpp.o:
- $(CXX) -c $(CC_FLAGS) $< -o $@ $(INCLUDES)
+ $(CXX) -std=c++14 -c $(CC_FLAGS) $< -o $@ $(INCLUDES)



.PHONY: clean
clean:
- rm ghostx
rm -f *.o
rm -f *~
+ rm ghostx
13 changes: 11 additions & 2 deletions recipes/ghostx/meta.yaml
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Expand Up @@ -8,16 +8,22 @@ package:
source:
url: http://www.bi.cs.titech.ac.jp/{{ name }}/releases/{{ name }}-{{ version }}.tar.gz
sha256: c2bd846e2d7c648931601578501db3aea89c4c5af8fa5f3fa79680c8fe0755bf
patches:
- ghostx-makefile.patch

build:
number: 1
number: 2
run_exports:
- {{ pin_subpackage(name, max_pin='x') }}

requirements:
build:
- make
- {{ compiler('c') }}
- {{ compiler('cxx') }}
run:
host:
- libgomp # [linux]
- llvm-openmp # [osx]

test:
commands:
Expand All @@ -30,6 +36,9 @@ about:
summary: "GHOSTX is a homology search tool which can detect remote homologues like BLAST and is about 100 times more efficient than BLAST by using suffix arrays. GHOSTX outputs search results in the format similar to BLAST-tabular format."

extra:
additional-platforms:
- linux-aarch64
- osx-arm64
recipe-maintainers:
- tomkinsc
identifiers:
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