bifrost: Parallel tool for de Bruijn graphs

[Jason W. Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Wed Oct 11 07:24:21 2023 -0500
Changeset:	c4660be7054bd482f53da2bb0186b8cad3e7bc90

Modified Files:
	Makefile
Added Files:
	bifrost/DESCR
	bifrost/Makefile
	bifrost/PLIST
	bifrost/distinfo
	bifrost/patches/patch-CMakeLists.txt
	bifrost/patches/patch-src_libpopcnt.h
	bifrost/patches/patch-src_strict__fstream.hpp

Log Message:
bifrost: Parallel tool for de Bruijn graphs

Bifrost is a tool and API for parallel construction, indexing and
querying of colored and compacted de Bruijn graphs from FASTA/FASTQ
DNA/RNA sequence files.

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=c4660be7054bd482f53da2bb0186b8cad3e7bc90

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 Makefile                                      |  1 +
 bifrost/DESCR                                 |  3 +++
 bifrost/Makefile                              | 27 +++++++++++++++++++++++++++
 bifrost/PLIST                                 |  1 +
 bifrost/distinfo                              |  8 ++++++++
 bifrost/patches/patch-CMakeLists.txt          | 12 ++++++++++++
 bifrost/patches/patch-src_libpopcnt.h         | 23 +++++++++++++++++++++++
 bifrost/patches/patch-src_strict__fstream.hpp | 15 +++++++++++++++
 8 files changed, 90 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 412744d655..83649beca5 100644
--- a/Makefile
+++ b/Makefile
@@ -265,6 +265,7 @@ SUBDIR+=	belle-sip
 SUBDIR+=	bertini
 SUBDIR+=	bfgminer
 SUBDIR+=	bicon
+SUBDIR+=	bifrost
 SUBDIR+=	bigdft
 SUBDIR+=	bijiben
 SUBDIR+=	bindgraph
diff --git a/bifrost/DESCR b/bifrost/DESCR
new file mode 100644
index 0000000000..68c41b2f44
--- /dev/null
+++ b/bifrost/DESCR
@@ -0,0 +1,3 @@
+Bifrost is a tool and API for parallel construction, indexing and
+querying of colored and compacted de Bruijn graphs from FASTA/FASTQ
+DNA/RNA sequence files.
diff --git a/bifrost/Makefile b/bifrost/Makefile
new file mode 100644
index 0000000000..f3685a4dde
--- /dev/null
+++ b/bifrost/Makefile
@@ -0,0 +1,27 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Wed Oct 11 07:14:48 CDT 2023               #
+###########################################################
+
+DISTNAME=	bifrost-1.3.0
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=pmelsted/}
+GITHUB_TAG=	v${PKGVERSION_NOREV}
+
+OWNER=		bacon%NetBSD.org@localhost
+HOMEPAGE=	https://github.com/pmelsted/bifrost
+COMMENT=	Parallel construction, indexing and querying of de Bruijn graphs
+LICENSE=	2-clause-bsd
+
+ONLY_FOR_PLATFORM=	 *-*-aarch64 *-*-x86_64 *-*-powerpc64 *-*-powerpc64le *-*-riscv64
+
+USE_LANGUAGES=	c c++
+USE_TOOLS+=	cmake
+USE_CMAKE=	yes
+CMAKE_ARGS+=	-DCOMPILATION_ARCH=${CPUTYPE:UOFF}
+
+# CentOS doesn't have zlib in the base, so uncomment if needed.
+# .include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/bifrost/PLIST b/bifrost/PLIST
new file mode 100644
index 0000000000..48d96a5493
--- /dev/null
+++ b/bifrost/PLIST
@@ -0,0 +1 @@
+@comment $NetBSD$
diff --git a/bifrost/distinfo b/bifrost/distinfo
new file mode 100644
index 0000000000..07a94535f8
--- /dev/null
+++ b/bifrost/distinfo
@@ -0,0 +1,8 @@
+$NetBSD$
+
+BLAKE2s (bifrost-1.3.0.tar.gz) = f4675731d2f5d4fc45a82992d8c59903c09266a8ae80d590d2590a3b3b3d0d94
+SHA512 (bifrost-1.3.0.tar.gz) = 43410775936988a6c52a5439e484ba066d9b47b018d6be29746801605cda9eec736571733832f3764d91aeb699d10facee1643a5151ab786b44dc30f7f88d434
+Size (bifrost-1.3.0.tar.gz) = 349405 bytes
+SHA1 (patch-CMakeLists.txt) = b67d3b9da75644d6c414988a1e034f4732d4ab5c
+SHA1 (patch-src_libpopcnt.h) = ebccf4b759d7cbfa25e88f4d1f016791eb87afee
+SHA1 (patch-src_strict__fstream.hpp) = 55e6c740fdcfbe749270953b7dd4ca19ac8b00c1
diff --git a/bifrost/patches/patch-CMakeLists.txt b/bifrost/patches/patch-CMakeLists.txt
new file mode 100644
index 0000000000..69e69a7820
--- /dev/null
+++ b/bifrost/patches/patch-CMakeLists.txt
@@ -0,0 +1,12 @@
+$NetBSD$
+
+--- CMakeLists.txt.orig	2023-08-12 14:26:29 UTC
++++ CMakeLists.txt
+@@ -46,7 +46,6 @@ else(CMAKE_BUILD_TYPE MATCHES Debug)
+ 		set(CMAKE_EXE_LINKER_FLAGS "-pg")
+ 	else(CMAKE_BUILD_TYPE MATCHES Profile)
+ 		message("Build type: Release")
+-		add_compile_options(-O3)
+ 	endif(CMAKE_BUILD_TYPE MATCHES Profile)
+ endif(CMAKE_BUILD_TYPE MATCHES Debug)
+ 
diff --git a/bifrost/patches/patch-src_libpopcnt.h b/bifrost/patches/patch-src_libpopcnt.h
new file mode 100644
index 0000000000..cb8f80ecee
--- /dev/null
+++ b/bifrost/patches/patch-src_libpopcnt.h
@@ -0,0 +1,23 @@
+$NetBSD$
+
+# Collision with libc popcount64
+
+--- src/libpopcnt.h.orig	2023-10-11 12:18:05.350259610 +0000
++++ src/libpopcnt.h
+@@ -105,6 +105,8 @@
+  * It uses 12 arithmetic operations, one of which is a multiply.
+  * http://en.wikipedia.org/wiki/Hamming_weight#Efficient_implementation
+  */
++
++#ifndef __NetBSD__	// Defined in libc
+ static inline uint64_t popcount64(uint64_t x)
+ {
+   uint64_t m1 = 0x5555555555555555ll;
+@@ -118,6 +120,7 @@ static inline uint64_t popcount64(uint64
+ 
+   return (x * h01) >> 56;
+ }
++#endif
+ 
+ #if defined(HAVE_ASM_POPCNT) && \
+     defined(__x86_64__)
diff --git a/bifrost/patches/patch-src_strict__fstream.hpp b/bifrost/patches/patch-src_strict__fstream.hpp
new file mode 100644
index 0000000000..6941247eff
--- /dev/null
+++ b/bifrost/patches/patch-src_strict__fstream.hpp
@@ -0,0 +1,15 @@
+$NetBSD$
+
+# Portability
+
+--- src/strict_fstream.hpp.orig	2023-10-10 13:54:08.000000000 +0000
++++ src/strict_fstream.hpp
+@@ -64,7 +64,7 @@ static std::string strerror()
+     } else {
+         return "Unknown error (" + std::to_string(err_num) + ")";
+     }
+-#elif ((_POSIX_C_SOURCE >= 200112L || _XOPEN_SOURCE >= 600) && ! _GNU_SOURCE) || defined(__APPLE__) || defined(__MUSL__)
++#elif ((_POSIX_C_SOURCE >= 200112L || _XOPEN_SOURCE >= 600) && ! _GNU_SOURCE) || defined(__APPLE__) || defined(__MUSL__) || defined(__FreeBSD__) || defined(__NetBSD__)
+ // XSI-compliant strerror_r()
+     const int err_num = errno; // See above
+     if (strerror_r(err_num, buff.data(), buff.size()) == 0) {