diff options
Diffstat (limited to 'biology/bifrost')
| -rw-r--r-- | biology/bifrost/Makefile | 23 | ||||
| -rw-r--r-- | biology/bifrost/distinfo | 3 | ||||
| -rw-r--r-- | biology/bifrost/files/patch-CMakeLists.txt | 10 | ||||
| -rw-r--r-- | biology/bifrost/pkg-descr | 3 | ||||
| -rw-r--r-- | biology/bifrost/pkg-plist | 53 |
5 files changed, 92 insertions, 0 deletions
diff --git a/biology/bifrost/Makefile b/biology/bifrost/Makefile new file mode 100644 index 000000000000..8820ddfa0631 --- /dev/null +++ b/biology/bifrost/Makefile @@ -0,0 +1,23 @@ +PORTNAME= bifrost +DISTVERSIONPREFIX= v +DISTVERSION= 1.3.5 +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= ${WRKSRC}/LICENSE + +ONLY_FOR_ARCHS= aarch64 amd64 powerpc64 powerpc64le riscv64 +ONLY_FOR_ARCHS_REASON= Requires a 64-bit processor + +USES= cmake +USE_GITHUB= yes + +CMAKE_ARGS= -DCOMPILATION_ARCH=${CPUTYPE:UOFF} + +GH_ACCOUNT= pmelsted + +.include <bsd.port.mk> diff --git a/biology/bifrost/distinfo b/biology/bifrost/distinfo new file mode 100644 index 000000000000..49f7e2d919bb --- /dev/null +++ b/biology/bifrost/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1710590640 +SHA256 (pmelsted-bifrost-v1.3.5_GH0.tar.gz) = e1b2491328b0cc1a32e433a8a9780f05547fa4b8d674b58abdda9ac8809f5341 +SIZE (pmelsted-bifrost-v1.3.5_GH0.tar.gz) = 356701 diff --git a/biology/bifrost/files/patch-CMakeLists.txt b/biology/bifrost/files/patch-CMakeLists.txt new file mode 100644 index 000000000000..27893b9ec44d --- /dev/null +++ b/biology/bifrost/files/patch-CMakeLists.txt @@ -0,0 +1,10 @@ +--- 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/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..9b4f28081aa5 --- /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/fastmod.h +include/bifrost/getRSS.h +include/bifrost/kseq.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 |