Rebuild muse recipe (bioconda#52157)

* Rebuild muse recipe

* try osx

* update patch

* clean up recipe

recipes/muse/fix-install_muse.sh.patch

@@ -1,8 +1,8 @@
 diff --git a/install_muse.sh b/install_muse.sh
-index 7bc2153..1ef4b13 100755
+index 7bc2153..8a57cf7 100755
 --- a/install_muse.sh
 +++ b/install_muse.sh
-@@ -4,13 +4,21 @@ make clean
+@@ -4,13 +4,20 @@ make clean
 
  mkdir -p lib
 
@@ -15,10 +15,10 @@ index 7bc2153..1ef4b13 100755
  # compile boost library
 -cd boost_1_70_0/
 -./bootstrap.sh
-+cd boost-1.86.0/
-+./bootstrap.sh --with-toolset="${TOOL}" --prefix="$(pwd)"
- ./b2 --clean
+-./b2 --clean
 -./b2
++cd boost-1.87.0.beta1/
++./bootstrap.sh --with-toolset="${TOOL}" --prefix="$(pwd)"
 +./b2 toolset="${TOOL}" --layout=system link=static \
 +	threading=multi strip=on \
 +	variant=release address-model=64 install
@@ -28,30 +28,42 @@ index 7bc2153..1ef4b13 100755
  cd ..
 
  # compile libtcmalloc
-@@ -22,12 +30,12 @@ fi
+@@ -22,12 +29,21 @@ fi
 
  git clone https://github.com/gperftools/gperftools.git
  cd gperftools
 -git checkout gperftools-2.9.1
-+git checkout gperftools-2.16
++git checkout gperftools-2.10
  ./autogen.sh
 -./configure --libdir="$PWD"
 -make -j4
-+./configure --libdir="${PWD}" --prefix="${PREFIX}"
-+make -j${CPU_COUNT}
- make install
+-make install
 -cp libtcmalloc_minimal.a ../lib/
++if [[ $(uname) == 'Darwin' ]]; then
++	export CFLAGS="$CFLAGS -D_XOPEN_SOURCE"
++	./configure --prefix="${PREFIX}" --libdir="${PWD}" \
++	--disable-debugalloc --disable-libunwind
++	make -j"${CPU_COUNT}"
++	make install
++else
++	./configure --prefix="${PREFIX}" --libdir="${PWD}" \
++	--enable-libunwind --enable-frame-pointers
++	make -j"${CPU_COUNT}"
++	make install
++fi
 +cp -f libtcmalloc_minimal.a ../lib/
  cd ..
 
  # combine htslib
-@@ -42,27 +50,19 @@ cd htslib
+@@ -41,28 +57,20 @@ git clone https://github.com/samtools/htslib.git
+ cd htslib
  git checkout 1.9
  #git submodule update --init --recursive
- autoreconf -i
+-autoreconf -i
 -./configure
 -make -j4
 -cp libhts.a ../lib/
++autoreconf -if
 +./configure --enable-libcurl --enable-plugins \
 +	LDFLAGS="-L${PREFIX}/lib -Wl,-R${PREFIX}/lib" \
 +	CPPFLAGS="-I${PREFIX}/include"
@@ -84,4 +96,4 @@ index 7bc2153..1ef4b13 100755
 
 +rm -rf htslib
 +rm -rf gperftools
-+rm -rf boost-1.86.0
++rm -rf boost-1.87.0.beta1

recipes/muse/meta.yaml

@@ -13,20 +13,19 @@ source:
     - 0001-Makefile.patch
     - fix-install_muse.sh.patch
     - version.patch
-- url: https://github.com/boostorg/boost/releases/download/boost-1.86.0/boost-1.86.0-b2-nodocs.tar.gz
-  sha256: 2128a4c96862b5c0970c1e34d76b1d57e4a1016b80df85ad39667f30b1deba26
-  folder: boost-1.86.0
+- url: https://github.com/boostorg/boost/releases/download/boost-1.87.0.beta1/boost-1.87.0.beta1-b2-nodocs.tar.gz
+  sha256: f12e906fde4c9d04d88c3aa821f00501817a37503441cbca8ce7852a2194aeb0
+  folder: boost-1.87.0.beta1
 
 build:
-  number: 1
+  number: 2
   skip: True  # [osx]
   run_exports:
     - {{ pin_subpackage('muse', max_pin="x") }}
 
 requirements:
   build:
     - {{ compiler('cxx') }}
-    - {{ compiler('c') }}
     - make
     - autoconf
     - automake
@@ -48,15 +47,17 @@ test:
     - 'MuSE 2>&1 | grep "Version"'
 
 about:
-  home: "https://github.com/wwylab/MuSE"
+  home: "https://bioinformatics.mdanderson.org/public-software/muse"
   license: "GPL-2.0-or-later"
   license_family: GPL
   license_file: "LICENSE"
   summary: "An accurate and ultra-fast somatic point mutation calling tool for whole-genome sequencing (WGS) and whole-exome sequencing (WES) data from heterogeneous tumor samples."
-  doc_url: "https://bioinformatics.mdanderson.org/public-software/muse"
+  doc_url: "https://github.com/wwylab/MuSE/blob/v{{ version }}/README.md"
   dev_url: "https://github.com/wwylab/MuSE"
 
 extra:
   identifiers:
     - doi:10.1101/gr.278456.123
     - doi:10.1186/s13059-016-1029-6
+  additional-platforms:
+    - linux-aarch64