remove osx skip

recipes/clair3/0001-Makefile.patch

@@ -0,0 +1,56 @@
+diff --git a/Makefile b/Makefile
+index 75e68b1..5de3a71 100644
+--- a/Makefile
++++ b/Makefile
+@@ -1,19 +1,19 @@
+ OS := $(shell uname)
+ ARCH := $(shell arch)
+
+-PYTHON ?= python3
++PYTHON ?= $(python)
+
+-all : libhts.a longphase libclair3.so
++all : libhts.a libclair3.so longphase
+ clean : clean_htslib clean_longphase clean_libclair3
+
+ SAMVER	=	1.15.1
+ LPVER	=	1.7.3
+-GCC	?=	gcc
+-GXX	?=	g++
+-PREFIX	?=	${CONDA_PREFIX}
+-LDFLAGS	=	-L ${PREFIX}/lib
+-CFLAGS	= -fpic -std=c99 -O3 -I ${PREFIX}/include -L ${PREFIX}/lib
+-CPPFLAGS	=	-std=c++11 -Wall -O3 -I ${PREFIX}/include -L ${PREFIX}/lib -Wl,-rpath=${PREFIX}/lib
++GCC	?=	$(CC)
++GXX	?=	$(CXX)
++PREFIX	?=	$(PREFIX)
++LDFLAGS	=	-L${PREFIX}/lib
++CFLAGS	= -fPIC -std=c11 -O3 -L${PREFIX}/lib
++CPPFLAGS	=	-std=c++14 -Wall -O3 -I${PREFIX}/include -Wl,-rpath=${PREFIX}/lib
+
+
+ samtools-$(SAMVER)/Makefile:
+@@ -24,9 +24,11 @@ samtools-$(SAMVER)/Makefile:
+ libhts.a: samtools-$(SAMVER)/Makefile
+ 	# this is required only to add in -fpic so we can build python module
+ 	@echo "\x1b[1;33mMaking $(@F)\x1b[0m"
+-	cd samtools-${SAMVER}/htslib-${SAMVER}; CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}" ./configure; make CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}"
++	cd samtools-${SAMVER}/htslib-${SAMVER}; autoreconf -if; CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}" ./configure; make CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}"
+ 	cp samtools-${SAMVER}/htslib-${SAMVER}/$@ $@
+
++libclair3.so: samtools-${SAMVER}/htslib-${SAMVER} libhts.a
++	${PYTHON} build.py
+
+ longphase:
+ 	curl -L -o longphase-${LPVER}.tar.xz https://github.com/twolinin/longphase/releases/download/v${LPVER}/longphase_linux-x64.tar.xz
+@@ -34,10 +36,6 @@ longphase:
+ 	mv longphase_linux-x64 $@
+ 	rm longphase-${LPVER}.tar.xz
+
+-
+-libclair3.so: samtools-${SAMVER}/htslib-${SAMVER} libhts.a
+-	${PYTHON} build.py
+-
+ src/%.o: src/%.c
+ 	$(GCC) -g -Isrc -Isamtools-${SAMVER}/htslib-${SAMVER} -c -pthread -fstack-protector-strong -D_FORTIFY_SOURCE=2 \
+ 		$(CFLAGS) $^ -o $@

recipes/clair3/0002-fpic.patch

@@ -0,0 +1,13 @@
+diff --git a/Makefile b/Makefile
+index 5de3a71..806ee28 100644
+--- a/Makefile
++++ b/Makefile
+@@ -12,7 +12,7 @@ GCC	?=	$(CC)
+ GXX	?=	$(CXX)
+ PREFIX	?=	$(PREFIX)
+ LDFLAGS	=	-L${PREFIX}/lib
+-CFLAGS	= -fPIC -std=c11 -O3 -L${PREFIX}/lib
++CFLAGS	= -std=c11 -O3 -L${PREFIX}/lib
+ CPPFLAGS	=	-std=c++14 -Wall -O3 -I${PREFIX}/include -Wl,-rpath=${PREFIX}/lib
+
+

recipes/clair3/build.sh

@@ -1,8 +1,15 @@
 #!/bin/bash
 
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export INCLUDE_PATH="${PREFIX}/include"
+export LIBRARY_PATH="${PREFIX}/lib"
+export CPATH="${PREFIX}/include"
+
 mkdir -pv $PREFIX/bin
-cp -rv clair3 models preprocess postprocess scripts shared $PREFIX/bin
-cp clair3.py $PREFIX/bin/
-cp run_clair3.sh $PREFIX/bin/
-make CC=${GCC} CXX=${GXX}  PREFIX=${PREFIX}
-cp  longphase libclair3* $PREFIX/bin
+cp -rf clair3 models preprocess postprocess scripts shared $PREFIX/bin
+install -v -m 0755 clair3.py $PREFIX/bin
+install -v -m 0755 run_clair3.sh $PREFIX/bin
+make all GCC="${CC}" GXX="${CXX}" PREFIX="${PREFIX}" python="${PYTHON}"
+
+install -v -m 0755 longphase $PREFIX/bin
+cp -rf libclair3* $PREFIX/bin

recipes/clair3/meta.yaml

@@ -8,25 +8,29 @@ package:
 source:
   url: http://www.bio8.cs.hku.hk/clair3/bioconda/Clair3_v{{ version }}.zip
   sha256: b2de8180d3825f9e1ed4ee1710ce0988dd85eba79ab8bdaf2ad8dae7ac70e228
+  patches:
+    - 0001-Makefile.patch
+    - 0002-fpic.patch  # [osx]
 
 build:
-  number: 0
-  skip: True  # [osx]
+  number: 1
   run_exports:
     - {{ pin_subpackage(name, max_pin="x") }}
 
 requirements:
   build:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
+    - autoconf
+    - automake
+    - make
+    - libtool
   host:
     - cffi
     - bzip2
     - xz
     - zlib
     - python 3.9.0
-    - automake
-    - make
     - libcurl 7.87.0
     - openssl 1.1.1
   run:
@@ -42,19 +46,28 @@ requirements:
     - zstd
     - openssl 1.1.1
     - cffi 1.14.4
+
 test:
   imports:
     - tensorflow
   commands:
     - longphase --version
     - which clair3.py
     - run_clair3.sh -v
-extra:
-  container:
-    extended-base: true
 
 about:
   home: 'https://github.com/HKU-BAL/Clair3'
   license: BSD-3-Clause
+  license_family: BSD
   license_file: LICENSE.md
   summary: "Clair3 is a small variant caller for long-reads. Compare to PEPPER (r0.4), Clair3 (v0.1) shows a better SNP F1-score with ≤30-fold of ONT data (precisionFDA Truth Challenge V2), and a better Indel F1-score, while runs generally four times faster. Clair3 makes the best of both worlds of using pileup or full-alignment as input for deep-learning based long-read small variant calling. Clair3 is simple and modular for easy deployment and integration."
+  dev_url: 'https://github.com/HKU-BAL/Clair3'
+  doc_url: "https://github.com/HKU-BAL/Clair3/blob/v{{ version }}/README.md"
+
+extra:
+  container:
+    extended-base: True
+  identifiers:
+    - doi:10.1038/s43588-022-00387-x
+    - biotools:clair3
+    - usegalaxy-eu:clair3