Update MuSE to latest version 2.1.2 (bioconda#47957)

* update version, change build number, change to sha256 * add run_exports * edit sha256 * clean up recipe * re-trigger CI * edit typo * add C compiler and openmp * add bzip2 * add xz * add make flags * add libcurl * edit build.sh * Pass the C++ env vars * Patch install_muse.sh Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> * add build reqs * move boost-cpp, htslib, and gperftools * add missing deps * edit dependencies * update to 2.1.1 * fix patch * coderabbit suggestions * update to 2.1.2 * add makefile patch * change to inc * add debug statements * edit patch * Update build.sh * edit build.sh * edit build.sh * Update fix-install_muse.sh.patch * edit build.sh * edit build.sh * edit build.sh * edit build.sh * edit build.sh * edit build.sh * edit build.sh * edit build.sh * edit build.sh * edit build.sh * edit build.sh * clean up recipe * edit makefile.patch * add patch * edit patches * add -ldl * edit build.sh * edit build.sh * skip osx x86_64 for now --------- Signed-off-by: Martin Tzvetanov Grigorov <[email protected]> Co-authored-by: Joshua Zhuang <[email protected]> Co-authored-by: mencian <[email protected]> Co-authored-by: Martin Grigorov <[email protected]> Co-authored-by: Martin Tzvetanov Grigorov <[email protected]> Co-authored-by: Ramprasad Neethiraj <[email protected]>
mencian · Nov 14, 2024 · c7ec561 · c7ec561
1 parent bda9210
commit c7ec561
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Showing 5 changed files with 204 additions and 23 deletions.
diff --git a/recipes/muse/0001-Makefile.patch b/recipes/muse/0001-Makefile.patch
@@ -0,0 +1,51 @@
+diff --git a/Makefile b/Makefile
+index 5edd6e1..78d946c 100755
+--- a/Makefile
++++ b/Makefile
+@@ -1,6 +1,6 @@
+-CPP := g++
+-CC := gcc
+-LINK := g++
++CPP := ${CXX}
++CC := ${CC}
++LINK := ${CXX}
+ mkfile_dir := $(dir $(abspath $(lastword $(MAKEFILE_LIST))))
+
+ CSOURCES= $(wildcard src/*.c)  
+@@ -11,12 +11,12 @@ COMMONOBJS= lib/libhts.a lib/libboost_iostreams.a lib/libtcmalloc_minimal.a
+ Warnings=-Wreturn-type -Warray-bounds -Wmaybe-uninitialized -Waddress
+ WarningsAsErrors=$(Warnings) -Werror=return-type -Werror=array-bounds -Werror=address
+ CFLAGS=  $(WarningsAsErrors) -Wno-unused-function
+-CPPFLAGS=  $(WarningsAsErrors) -Wno-unused-function -std=c++11
++CPPFLAGS=  $(WarningsAsErrors) -Wno-unused-function -std=c++14
+
+ RELEASE_FLAGS= -O3 -g
+
+ # Includes
+-INCLUDES = -Iinc/
++INCLUDES += -Iinc/ -Iinc/htslib -I$(PREFIX)/include
+ #
+ # Common flags
+ COMMONFLAGS += $(INCLUDES)
+@@ -24,7 +24,7 @@ COMMONFLAGS += $(INCLUDES)
+ CXXFLAGS += $(COMMONFLAGS)
+ CFLAGS += $(COMMONFLAGS)
+ CPPFLAGS += $(COMMONFLAGS)
+-COMMONLIBS= -Llib/ -lz -lm -lpthread -lbz2 -lcurl -lcrypto -llzma -fopenmp
++COMMONLIBS += -Llib/ -lz -lm -lpthread -lbz2 -lcurl -lcrypto -llzma -lhts -ldl -fopenmp -L${PREFIX}/lib
+
+ #LIBS += $(COMMONLIBS) -ltcmalloc
+ LIBS += $(COMMONLIBS)
+@@ -38,10 +38,10 @@ all: $(TARGET)
+ .SUFFIXES: .c .cpp .o
+
+ %.c.o: %.c
+-	$(CC) $(CFLAGS) $(RELEASE_FLAGS) -c $< -o $@
++	$(CC) $(CFLAGS) $(RELEASE_FLAGS) $(INCLUDES) $(LIBS) -c $< -o $@
+
+ %.cpp.o: %.cpp
+-	$(CPP) $(CPPFLAGS) $(RELEASE_FLAGS) $(OPENMP) -c $< -o $@
++	$(CPP) $(CPPFLAGS) $(RELEASE_FLAGS) $(OPENMP) $(INCLUDES) $(LIBS) -c $< -o $@
+
+ $(TARGET): $(OBJS) Makefile
+ 	$(LINKLINE)
diff --git a/recipes/muse/0001-add-LDFLAGS.patch b/recipes/muse/0001-add-LDFLAGS.patch
diff --git a/recipes/muse/build.sh b/recipes/muse/build.sh
@@ -1,6 +1,29 @@
-#!/usr/bin/env bash
+#!/bin/bash
+set -euo pipefail
 
-make CPP="${CXX}" CPPFLAGS="${CXXFLAGS}"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CFLAGS="${CFLAGS} -O3"
 
-mkdir -p "${PREFIX}/bin"
-cp MuSE "${PREFIX}/bin/"
+rm -rf boost_1_70_0/
+
+if [[ `uname` == "Darwin" ]]; then
+	ln -sf ${CC} ${PREFIX}/bin/clang
+	ln -sf ${CXX} ${PREFIX}/bin/clang++
+else
+	ln -sf ${CC} ${PREFIX}/bin/gcc
+	ln -sf ${CXX} ${PREFIX}/bin/g++
+fi
+
+./install_muse.sh
+
+if [[ `uname` == "Darwin" ]]; then
+	rm -rf ${PREFIX}/bin/clang
+	rm -rf ${PREFIX}/bin/clang++
+else
+	rm -rf ${PREFIX}/bin/gcc
+	rm -rf ${PREFIX}/bin/g++
+fi
+
+install -d "${PREFIX}/bin"
+install -v -m 0755 MuSE "${PREFIX}/bin"
diff --git a/recipes/muse/fix-install_muse.sh.patch b/recipes/muse/fix-install_muse.sh.patch
@@ -0,0 +1,84 @@
+diff --git a/install_muse.sh b/install_muse.sh
+index 7bc2153..f8ab6e3 100755
+--- a/install_muse.sh
++++ b/install_muse.sh
+@@ -4,13 +4,21 @@ make clean
+
+ mkdir -p lib
+
++if [[ `uname` == "Darwin" ]]; then
++	export TOOL=clang
++else
++	export TOOL=gcc
++fi
++
+ # compile boost library
+-cd boost_1_70_0/
+-./bootstrap.sh
++cd boost-1.86.0/
++./bootstrap.sh --with-toolset="${TOOL}" --prefix="${PREFIX}"
+ ./b2 --clean
+-./b2
++./b2 toolset="${TOOL}" --layout=system link=static \
++	threading=multi strip=on include="${PREFIX}/include" \
++	variant=release address-model=64 install
+
+-cp stage/lib/libboost_iostreams.a ../lib/
++cp -f ${PREFIX}/lib/libboost_iostreams.a ../lib/
+ cd ..
+
+ # compile libtcmalloc
+@@ -22,12 +30,12 @@ fi
+
+ git clone https://github.com/gperftools/gperftools.git
+ cd gperftools
+-git checkout gperftools-2.9.1
++git checkout gperftools-2.16
+ ./autogen.sh
+-./configure --libdir="$PWD"
+-make -j4
++./configure --libdir="${PWD}" --prefix="${PREFIX}"
++make -j${CPU_COUNT}
+ make install
+-cp libtcmalloc_minimal.a ../lib/
++cp -f libtcmalloc_minimal.a ../lib/
+ cd ..
+
+ # combine htslib
+@@ -42,27 +50,15 @@ cd htslib
+ git checkout 1.9
+ #git submodule update --init --recursive
+ autoreconf -i
+-./configure
+-make -j4
+-cp libhts.a ../lib/
++./configure --enable-libcurl --enable-plugins \
++	LDFLAGS="-L${PREFIX}/lib -Wl,-R${PREFIX}/lib" \
++	CPPFLAGS="-I${PREFIX}/include"
++make -j${CPU_COUNT}
++cp -f libhts.a ../lib/
+
+ cd ..
+
+-make
+-
+-#clean htslib and gperftools and boost libraries
+-rm -r boost_1_70_0/stage
+-
+-chmod -R 755 gperftools
+-rm -r gperftools
+-
+-chmod -R 755 htslib
+-rm -r htslib
+-
+-
+-
+-
+-
+-
+-
+-
++CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" \
++    CC="${CC}" CXX="${CXX}" CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" \
++    LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" \
++    make -j"${CPU_COUNT}"
diff --git a/recipes/muse/meta.yaml b/recipes/muse/meta.yaml
@@ -1,31 +1,61 @@
+{% set name = "MuSE" %}
+{% set version = "2.1.2" %}
+{% set sha256 = "48df7ec3f64244400243163b48eb658105854b7b0d6287af98242dd89f396f59" %}
+
 package:
-  name: muse
-  version: 1.0.rc
+  name: {{ name|lower }}
+  version: {{ version }}
 
 source:
-  md5: c63fdb48c041f6f9545879f1a7e4da58
-  url: https://github.com/danielfan/MuSE/archive/v1.0-rc.tar.gz
+- url: https://github.com/wwylab/MuSE/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: {{ sha256 }}
   patches:
-    - 0001-add-LDFLAGS.patch
+    - 0001-Makefile.patch
+    - fix-install_muse.sh.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
 
 build:
-  number: 8
+  number: 0
+  skip: True  # [osx]
+  run_exports:
+    - {{ pin_subpackage('muse', max_pin="x") }}
 
 requirements:
   build:
-    - make
     - {{ compiler('cxx') }}
     - {{ compiler('c') }}
+    - make
+    - autoconf
+    - automake
+    - libtool
   host:
+    - llvm-openmp  # [osx]
+    - libgomp  # [linux]
+    - libcurl
+    - icu
+    - bzip2
+    - xz
     - zlib
   run:
-    - zlib
+    - llvm-openmp  # [osx]
+    - libgomp  # [linux]
 
 test:
   commands:
-    - MuSE 2>&1 | grep Version > /dev/null
+    - "MuSE 2>&1 | grep Version > /dev/null"
 
 about:
-  home: "http://bioinformatics.mdanderson.org/main/MuSE"
-  license: "https://github.com/danielfan/MuSE/blob/master/LICENSE"
-  summary: Somatic point mutation caller
+  home: "https://github.com/wwylab/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"
+  dev_url: "https://github.com/wwylab/MuSE"
+
+extra:
+  identifiers:
+    - doi:10.1101/gr.278456.123
+    - doi:10.1186/s13059-016-1029-6