Date: Fri, 7 Jul 2023 13:38:24 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 964411795080 - main - biology/bifrost: Parallel tool for de Bruijn graphs Message-ID: <202307071338.367DcOZJ084007@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=964411795080849c96f95a7ce315e1b230b9b93a commit 964411795080849c96f95a7ce315e1b230b9b93a Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2023-07-07 13:37:33 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2023-07-07 13:38:22 +0000 biology/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. --- biology/Makefile | 1 + biology/bifrost/Makefile | 18 ++++++++ biology/bifrost/distinfo | 3 ++ .../bifrost/files/patch-src_strict__fstream.hpp | 11 +++++ biology/bifrost/pkg-descr | 3 ++ biology/bifrost/pkg-plist | 53 ++++++++++++++++++++++ 6 files changed, 89 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index c8654fab2077..fe34cafefca7 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -15,6 +15,7 @@ SUBDIR += bcftools SUBDIR += bedtools SUBDIR += bfc + SUBDIR += bifrost SUBDIR += bio-mocha SUBDIR += bioawk SUBDIR += biococoa diff --git a/biology/bifrost/Makefile b/biology/bifrost/Makefile new file mode 100644 index 000000000000..1ca58622a09a --- /dev/null +++ b/biology/bifrost/Makefile @@ -0,0 +1,18 @@ +PORTNAME= bifrost +DISTVERSIONPREFIX= v +DISTVERSION= 1.2.1 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Parallel construction, indexing and querying of de Bruijn graphs +WWW= https://github.com/pmelsted/bifrost + +LICENSE= BSD2CLAUSE +LICENSE_FILE= ${WRKSRC}/LICENSE + +USES= cmake +USE_GITHUB= yes + +GH_ACCOUNT= pmelsted + +.include <bsd.port.mk> diff --git a/biology/bifrost/distinfo b/biology/bifrost/distinfo new file mode 100644 index 000000000000..f92944f13d87 --- /dev/null +++ b/biology/bifrost/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1688397139 +SHA256 (pmelsted-bifrost-v1.2.1_GH0.tar.gz) = fe93080ef3ea71ff009fc206b5c17dd40fbfd18293000621a83d7d947dfedf1a +SIZE (pmelsted-bifrost-v1.2.1_GH0.tar.gz) = 905438 diff --git a/biology/bifrost/files/patch-src_strict__fstream.hpp b/biology/bifrost/files/patch-src_strict__fstream.hpp new file mode 100644 index 000000000000..e3b3caf35931 --- /dev/null +++ b/biology/bifrost/files/patch-src_strict__fstream.hpp @@ -0,0 +1,11 @@ +--- src/strict_fstream.hpp.orig 2023-07-03 15:14:36 UTC ++++ 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__) + // XSI-compliant strerror_r() + const int err_num = errno; // See above + if (strerror_r(err_num, buff.data(), buff.size()) == 0) { diff --git a/biology/bifrost/pkg-descr b/biology/bifrost/pkg-descr new file mode 100644 index 000000000000..68c41b2f44fc --- /dev/null +++ b/biology/bifrost/pkg-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/biology/bifrost/pkg-plist b/biology/bifrost/pkg-plist new file mode 100644 index 000000000000..7d555618743c --- /dev/null +++ b/biology/bifrost/pkg-plist @@ -0,0 +1,53 @@ +bin/Bifrost +include/bifrost/BitContainer.hpp +include/bifrost/BlockedBloomFilter.hpp +include/bifrost/ColorSet.hpp +include/bifrost/ColoredCDBG.hpp +include/bifrost/ColoredCDBG.tcc +include/bifrost/Common.hpp +include/bifrost/CompactedDBG.hpp +include/bifrost/CompactedDBG.tcc +include/bifrost/CompressedCoverage.hpp +include/bifrost/CompressedSequence.hpp +include/bifrost/DataAccessor.hpp +include/bifrost/DataAccessor.tcc +include/bifrost/DataManager.hpp +include/bifrost/DataStorage.hpp +include/bifrost/DataStorage.tcc +include/bifrost/FASTX_Parser.hpp +include/bifrost/File_Parser.hpp +include/bifrost/GFA_Parser.hpp +include/bifrost/IO.tcc +include/bifrost/Kmer.hpp +include/bifrost/KmerCovIndex.hpp +include/bifrost/KmerCovIndex.tcc +include/bifrost/KmerHashTable.hpp +include/bifrost/KmerIterator.hpp +include/bifrost/KmerStream.hpp +include/bifrost/Lock.hpp +include/bifrost/MinimizerIndex.hpp +include/bifrost/NeighborIterator.hpp +include/bifrost/NeighborIterator.tcc +include/bifrost/RepHash.hpp +include/bifrost/Search.tcc +include/bifrost/StreamCounter.hpp +include/bifrost/TinyBitmap.hpp +include/bifrost/TinyVector.hpp +include/bifrost/Unitig.hpp +include/bifrost/UnitigIterator.hpp +include/bifrost/UnitigIterator.tcc +include/bifrost/UnitigMap.hpp +include/bifrost/UnitigMap.tcc +include/bifrost/getRSS.h +include/bifrost/kseq.h +include/bifrost/libdivide.h +include/bifrost/libpopcnt.h +include/bifrost/minHashIterator.hpp +include/bifrost/roaring.h +include/bifrost/roaring.hh +include/bifrost/rw_spin_lock.h +include/bifrost/strict_fstream.hpp +include/bifrost/wyhash.h +include/bifrost/zstr.hpp +lib/libbifrost.a +lib/libbifrost.so
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