Update svdss to 2.1.1 (#64326)

* Update svdss to 2.1.1

* Update meta.yaml

* Update meta.yaml

* Update meta.yaml

* Update cmake.patch

* Delete recipes/svdss/cmake.patch

* Update build.sh

* Update meta.yaml

---------

Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>

Author: BiocondaBot

recipes/svdss/build.sh

@@ -1,30 +1,32 @@
 #!/bin/bash
 
-mkdir -p ${PREFIX}/bin
+mkdir -p "${PREFIX}/bin"
+
 export INCLUDE_PATH="${PREFIX}/include"
 export LIBRARY_PATH="${PREFIX}/lib"
 export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
 export CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include"
 export CFLAGS="${CFLAGS} -O3 -L${PREFIX}/lib"
 export CXXFLAGS="${CXXFLAGS} -O3"
 
-if [[ `uname` == "Darwin" ]]; then
+if [[ `uname -s` == "Darwin" ]]; then
 	export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
 	sed -i.bak 's|libhts.so|libhts.dylib|' CMakeLists.txt
 	sed -i.bak 's|libdeflate.so|libdeflate.dylib|' CMakeLists.txt
 	sed -i.bak 's|sed -i|sed -i.bak|' CMakeLists.txt
-	rm -rf *.bak
+	rm -f *.bak
 else
 	export CONFIG_ARGS=""
 fi
 
-cmake -S. -B build -DCMAKE_BUILD_TYPE=Release \
+cmake -S . -B build -DCMAKE_BUILD_TYPE=Release \
 	-DCONDAPREFIX="${PREFIX}" -DCMAKE_CXX_COMPILER="${CXX}" \
 	-DCMAKE_CXX_FLAGS="${CXXFLAGS}" -DCMAKE_C_COMPILER="${CC}" \
 	-DCMAKE_C_FLAGS="${CFLAGS}" \
+	-DARCH="$(uname -m)" \
+	-DOS="$(uname -s)" \
 	-Wno-dev -Wno-deprecated --no-warn-unused-cli \
 	"${CONFIG_ARGS}"
 cmake --build build -j "${CPU_COUNT}"
 
-install -v -m 0755 SVDSS ${PREFIX}/bin
-install -v -m 0755 run_svdss ${PREFIX}/bin
+install -v -m 0755 SVDSS run_svdss "${PREFIX}/bin"

recipes/svdss/cmake.patch

@@ -1,5 +1,5 @@
-{% set version = "2.1.0" %}
-{% set sha256 = "32dc3cdb3c8aec25a855b9dbcd09a7274a0bd95a94db11fb4f94567f35b98b90" %}
+{% set version = "2.1.1" %}
+{% set sha256 = "c73df403c9a6bd1463d627e50a0d94a9743daff0385d3aa98df89416ab0a349e" %}
 
 package:
   name: svdss
@@ -8,8 +8,6 @@ package:
 source:
   url: https://github.com/Parsoa/SVDSS/archive/refs/tags/v{{ version }}.tar.gz
   sha256: {{ sha256 }}
-  patches:
-    - cmake.patch
 
 build:
   number: 0
@@ -57,8 +55,15 @@ about:
   doc_url: "https://github.com/Parsoa/SVDSS/blob/v{{ version }}/README.md"
 
 extra:
+  #cli.c:(.text+0x11e8): undefined reference to `ksw_gg2_sse'
+  #src/abpoa/src/simd_instruction.h:21:10: fatal error: immintrin.h: No such file or directory
+  #include <immintrin.h>
+  #additional-platforms:
+    #- linux-aarch64
   identifiers:
     - biotools:svdss
     - doi:10.1038/s41592-022-01674-1
   recipe-maintainers:
     - ldenti
+  skip-lints:
+    - compiler_needs_stdlib_c