ghostx: add aarch64/arm64 builds (#52967)

* ghostx: add aarch64/arm64 builds Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * ghostx: Patch the Makefile to be able to use custom CC and CXX Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Add '-D_LIBCPP_DISABLE_AVAILABILITY' for OSX Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Add libgomp/llvm-openmp as host deps Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Set C++ standard to 14 Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Try without libgomp/llvm-openmp Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * Re-add libgomp/llvm-openmp Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> --------- Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
bioconda · Dec 23, 2024 · 0ca83c0 · 0ca83c0
1 parent a0ec37f
commit 0ca83c0
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Showing 4 changed files with 57 additions and 6 deletions.
diff --git a/build-fail-blacklist b/build-fail-blacklist
@@ -607,7 +607,6 @@ recipes/fastuniq
 recipes/fgap
 recipes/funcannot
 recipes/genepender
-recipes/ghostx
 recipes/ls-gkm
 recipes/mosaik
 recipes/ngmerge

diff --git a/recipes/ghostx/build.sh b/recipes/ghostx/build.sh
@@ -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 $PREFIX/bin
diff --git a/recipes/ghostx/ghostx-makefile.patch b/recipes/ghostx/ghostx-makefile.patch
@@ -0,0 +1,39 @@
+diff --git i/src/Makefile w/src/Makefile
+index 8844e0a..3248657 100644
+--- i/src/Makefile
++++ w/src/Makefile
+@@ -1,9 +1,9 @@
+ LAST_CC=g++
+-CC=gcc
+-CXX=g++
++CC?=gcc
++CXX?=g++
+ COMMON_FLAGS=-Wall -Wextra -pedantic -fopenmp -O3
+ INCLUDES = -I ../ext/boost
+-CC_FLAGS=${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
diff --git a/recipes/ghostx/meta.yaml b/recipes/ghostx/meta.yaml
@@ -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:
@@ -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: