diff options
author | Jason W. Bacon <jwb@FreeBSD.org> | 2023-07-07 13:37:33 +0000 |
---|---|---|
committer | Jason W. Bacon <jwb@FreeBSD.org> | 2023-07-07 13:38:22 +0000 |
commit | 964411795080849c96f95a7ce315e1b230b9b93a (patch) | |
tree | 98a820a584dae2b502fecd0c78d1c3eb665b6c2d /biology/bifrost | |
parent | 062481165673585a01a42f1ba5689b04e923f6c7 (diff) | |
download | ports-964411795080849c96f95a7ce315e1b230b9b93a.tar.gz ports-964411795080849c96f95a7ce315e1b230b9b93a.zip |
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.
Diffstat (limited to 'biology/bifrost')
-rw-r--r-- | biology/bifrost/Makefile | 18 | ||||
-rw-r--r-- | biology/bifrost/distinfo | 3 | ||||
-rw-r--r-- | biology/bifrost/files/patch-src_strict__fstream.hpp | 11 | ||||
-rw-r--r-- | biology/bifrost/pkg-descr | 3 | ||||
-rw-r--r-- | biology/bifrost/pkg-plist | 53 |
5 files changed, 88 insertions, 0 deletions
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 |