Update usher to 0.6.4

recipes/usher/build.sh

@@ -2,25 +2,36 @@
 #/System/Volumes/Data/System/DriverKit/usr/lib/libSystem.dylib
 mkdir -p $PREFIX/bin
 
+export INCLUDES="-I${PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
 
 if [[ "$OSTYPE" == "darwin"* ]]; then
     curl -sSLO https://github.com/oneapi-src/oneTBB/releases/download/2019_U9/tbb2019_20191006oss_mac.tgz
     tar -xzf tbb2019_20191006oss_mac.tgz
     tbb_root=tbb2019_20191006oss
+    export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
 else
     curl -sSLO https://github.com/oneapi-src/oneTBB/archive/2019_U9.tar.gz
     tar -xzf 2019_U9.tar.gz
     tbb_root=oneTBB-2019_U9
+    export CONFIG_ARGS=""
 fi
 
 mkdir -p build
 pushd build
 
-cmake -DTBB_DIR=${PWD}/../$tbb_root -DCMAKE_PREFIX_PATH=${PWD}/../$tbb_root/cmake -DCMAKE_INSTALL_PREFIX=${PREFIX} ..
+cmake -S .. -B . -DCMAKE_INSTALL_PREFIX=${PREFIX} \
+    -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER="${CXX}" \
+    -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \
+    -DTBB_DIR=${PWD}/../$tbb_root \
+    -DCMAKE_PREFIX_PATH=${PWD}/../$tbb_root/cmake \
+    "${CONFIG_ARGS}"
 
 if [[ "$OSTYPE" == "darwin"* ]]; then
     # omit ripples-fast due to problems building on Mac
-    make -j 1 usher matUtils matOptimize usher-sampled ripples
+    make -j"${CPU_COUNT}" usher matUtils matOptimize usher-sampled ripples
     cat > ripples-fast <<EOF
 #!/bin/bash
 # This is a placeholder for the program ripples-fast on Mac where the build is currently failing.
@@ -34,7 +45,7 @@ echo ""
 EOF
     chmod a+x ripples-fast
 else
-    make -j 1
+    cmake --build . --target install -j "${CPU_COUNT}"
 fi
 
 cp ./usher ${PREFIX}/bin/

recipes/usher/meta.yaml

@@ -1,15 +1,16 @@
-{% set version="0.6.3" %}
+{% set name = "usher" %}
+{% set version = "0.6.4" %}
 
 package:
-  name: usher
+  name: {{ name }}
   version: {{ version }}
 
 source:
   - url: https://github.com/yatisht/usher/archive/v{{ version  }}.tar.gz
-    sha256: 95aba8f748599915f21f7bdf883c2e532f2d821138f06cb2e4e58d7323019946
+    sha256: f9c38f7bf65ec22f22620917ec3c4c99fc23e96cbd75c03f104a8b03533674fd
 
 build:
-  number: 2
+  number: 0
   run_exports:
     - {{ pin_subpackage('usher', max_pin="x.x") }}
 
@@ -20,13 +21,13 @@ requirements:
     - cmake
     - {{ compiler('cxx') }}
     - {{ compiler('c') }}
-    - wget
   host:
     - boost-cpp
     - libprotobuf
     - openmpi =4.1.2
     - openssh
     - isa-l
+    - wget
   run:
     - mafft
     - boost-cpp
@@ -47,11 +48,15 @@ about:
   license: MIT
   license_family: MIT
   license_file: LICENSE
-  summary: Ultrafast Sample Placement on Existing Trees (UShER)
-  doc_url: https://usher-wiki.readthedocs.io/en/latest/
+  summary: "Ultrafast Sample Placement on Existing Trees (UShER)."
+  doc_url: https://usher-wiki.readthedocs.io/en/latest
+  dev_url: https://github.com/yatisht/usher
 
 extra:
   additional-platforms:
     - linux-aarch64
   identifiers:
     - doi:10.1038/s41588-021-00862-7
+    - biotools:usher
+    - usegalaxy-eu:usher_matutils
+    - usegalaxy-eu:usher