clean up recipe

bioconda · Nov 18, 2024 · 219165f · 219165f
1 parent 7f9c3c4
commit 219165f
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Showing 2 changed files with 39 additions and 36 deletions.
diff --git a/recipes/libmaus2/build.sh b/recipes/libmaus2/build.sh
@@ -3,15 +3,12 @@ set -eu
 export LIBS="-lstdc++fs -lcurl -lz -ldeflate"
 
 autoreconf -if
-autoupdate
 ./configure --prefix="${PREFIX}" CXX="${CXX}" CC="${CC}" \
 	LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" \
 	CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include" \
 	--with-snappy --with-io_lib --with-libdeflate \
 	--with-libsecrecy --with-nettle \
 	--with-lzma --with-gmp
 
-cat config.log
-
 make -j"${CPU_COUNT}"
 make install
diff --git a/recipes/libmaus2/patch b/recipes/libmaus2/patch
@@ -127,36 +127,6 @@ index 134ff0f4..b8fcfe88 100644
 
  				setHWTReq  (p_hwt_req.string());
  				setHWT     (p_hwt.string());
-diff --git a/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp b/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
-index 1e8e53b9..a91d1916 100644
---- a/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
-+++ b/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
-@@ -111,11 +111,11 @@ namespace libmaus2
- 				// base tmp directory name
- 				std::string tmpdirname;
- 				// tmpdirname as path object
--				std::filesystem::path tmppath;
--				std::filesystem::path base_tmp_path;
--				std::filesystem::path ds_tmp_path_base_ds_tmp;
--				std::filesystem::path merge_tmp_path;
--				std::filesystem::path ds_tmp_path_merge_ds_tmp;
-+				std::experimental::filesystem::path tmppath;
-+				std::experimental::filesystem::path base_tmp_path;
-+				std::experimental::filesystem::path ds_tmp_path_base_ds_tmp;
-+				std::experimental::filesystem::path merge_tmp_path;
-+				std::experimental::filesystem::path ds_tmp_path_merge_ds_tmp;
-
- 				std::unique_ptr<libmaus2::util::DirectoryStructure> DSbase;
- 				std::unique_ptr<libmaus2::util::DirectoryStructure> DSmerge;
-@@ -333,7 +333,7 @@ namespace libmaus2
- 					return C;
- 				}
-
--				static std::filesystem::path ensureDirectory(std::filesystem::path path)
-+				static std::experimental::filesystem::path ensureDirectory(std::experimental::filesystem::path path)
- 				{
- 					libmaus2::aio::OutputStreamFactoryContainer::mkdirp(path.string(),0700);
- 					return path;
 diff --git a/src/libmaus2/util/ArgInfo.cpp b/src/libmaus2/util/ArgInfo.cpp
 index 3802cbb7..8ecd441c 100644
 --- a/src/libmaus2/util/ArgInfo.cpp
@@ -267,6 +237,42 @@ index 2ff71e4a..0714e612 100644
  				dictpath /= digest;
 
  				std::cerr << "[V] writing " << dictpath << " for " << pat.sid << " in " << ref << std::endl;
--- 
-2.33.0
-
+diff --git a/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp b/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
+index 180f466..0b69f74 100644
+--- a/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
++++ b/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
+@@ -111,11 +111,11 @@ namespace libmaus2
+ 				// base tmp directory name
+ 				std::string tmpdirname;
+ 				// tmpdirname as path object
+-				std::filesystem::path tmppath;
+-				std::filesystem::path base_tmp_path;
+-				std::filesystem::path ds_tmp_path_base_ds_tmp;
+-				std::filesystem::path merge_tmp_path;
+-				std::filesystem::path ds_tmp_path_merge_ds_tmp;
++				std::experimental::filesystem::path tmppath;
++				std::experimental::filesystem::path base_tmp_path;
++				std::experimental::filesystem::path ds_tmp_path_base_ds_tmp;
++				std::experimental::filesystem::path merge_tmp_path;
++				std::experimental::filesystem::path ds_tmp_path_merge_ds_tmp;
+
+ 				std::unique_ptr<libmaus2::util::DirectoryStructure> DSbase;
+ 				std::unique_ptr<libmaus2::util::DirectoryStructure> DSmerge;
+@@ -333,7 +333,7 @@ namespace libmaus2
+ 					return C;
+ 				}
+
+-				static std::filesystem::path ensureDirectory(std::filesystem::path path)
++				static std::experimental::filesystem::path ensureDirectory(std::experimental::filesystem::path path)
+ 				{
+ 					libmaus2::aio::OutputStreamFactoryContainer::mkdirp(path.string(),0700);
+ 					return path;
+@@ -358,7 +358,7 @@ namespace libmaus2
+ 					preisasamplingrate(std::min(options.maxpreisasamplingrate,blocksizeprevtwo)),
+ 					V_boundedlcpblockvalues(new libmaus2::util::AtomicArray<uint64_t>(numblocks,0)),
+ 					// tmp directory name
+-					tmpdirname(ensureDirectory(std::filesystem::path(options.tmpfilenamebase + "_tmpdir")).string()),
++					tmpdirname(ensureDirectory(std::experimental::filesystem::path(options.tmpfilenamebase + "_tmpdir")).string()),
+ 					// path object for tmp directory name
+ 					tmppath(tmpdirname),
+ 					base_tmp_path(ensureDirectory(tmppath / "base_tmp")),