biology/abyss 2.3.10_1 FreeBSD
Assembly By Short Sequences: parallel, paired-end sequence assembler
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- License
- GPLv3
- Categories
- biology
- Package size
- 1469.2 KiB, 6821.6 KiB installed
Description
ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.
Install
Binary package:
pkg install abyssFrom the ports tree:
cd /usr/ports/biology/abyss/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= abyss>0:biology/abyssPackages
The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.
| Repository | aarch64 | amd64 | armv6 | armv7 | i386 |
|---|---|---|---|---|---|
| FreeBSD:14:latest | 2.3.10_1 | 2.3.10_1 | - | - | - |
| FreeBSD:14:quarterly | 2.3.10_1 | 2.3.10_1 | n/a | - | - |
| FreeBSD:15:latest | 2.3.10_1 | 2.3.10_1 | n/a | - | - |
| FreeBSD:15:quarterly | 2.3.10_1 | 2.3.10_1 | n/a | n/a | n/a |
| FreeBSD:16:latest | 2.3.10_1 | 2.3.10_1 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependencies
As this port's Makefile names them.
Build 3
${LOCALBASE}/include/boost/version.hpp: devel/boost-libsghc: lang/ghcpandoc: textproc/hs-pandoc
Library 4
libbtllib.so: biology/btlliblibffi.so: devel/libffilibgmp.so: math/gmplibmpich.so: net/mpich
Runtime 2
bash: shells/bashgmake: devel/gmake
The full lists below include those, and their dependencies in turn.
Build dependencies 47
- archivers/brotli
- archivers/libdeflate
- archivers/liblz4
- archivers/zstd
- biology/btllib
- biology/htslib
- biology/samtools
- converters/libiconv
- databases/sqlite3
- devel/autoconf
- devel/autoconf-switch
- devel/automake
- devel/binutils
- devel/boost-libs
- devel/gettext-runtime
- devel/gmake
- devel/hwloc2
- devel/icu
- devel/json-c
- devel/level-zero
- devel/libedit
- devel/libepoll-shim
- devel/libffi
- devel/libpciaccess
- devel/libunistring
- devel/m4
- devel/readline
- devel/sdsl-lite
- dns/libidn2
- dns/libpsl
- ftp/curl
- lang/gcc14
- lang/ghc
- lang/perl5.42
- lang/tcl86
- math/gmp
- math/libtommath
- math/mpc
- math/mpfr
- misc/hwdata
- net/libfabric
- net/mpich
- print/indexinfo
- security/libssh2
- textproc/hs-pandoc
- textproc/libxml2
- www/libnghttp2
Run dependencies 40
- archivers/brotli
- archivers/libdeflate
- archivers/liblz4
- archivers/zstd
- biology/btllib
- biology/htslib
- biology/samtools
- converters/libiconv
- databases/sqlite3
- devel/binutils
- devel/gettext-runtime
- devel/gmake
- devel/hwloc2
- devel/json-c
- devel/level-zero
- devel/libedit
- devel/libepoll-shim
- devel/libffi
- devel/libpciaccess
- devel/libunistring
- devel/readline
- devel/sdsl-lite
- dns/libidn2
- dns/libpsl
- ftp/curl
- lang/gcc14
- lang/perl5.42
- lang/tcl86
- math/gmp
- math/libtommath
- math/mpc
- math/mpfr
- misc/hwdata
- net/libfabric
- net/mpich
- print/indexinfo
- security/libssh2
- shells/bash
- textproc/libxml2
- www/libnghttp2
No port depends on this one.
Configuration
Options name: biology_abyss
| Option | Default | Description |
|---|---|---|
| DOCS | off | Build and/or install documentation |
- USES
- autoreconf compiler:c++11-lang gmake iconv:wchar_t localbase:ldflags shebangfix sqlite
- Service scripts
- none
Files
Manual pages 1
- abyss-sealer(1)
pkg-plist 58
- bin/ABYSS
- bin/ABYSS-P
- bin/AdjList
- bin/Consensus
- bin/DAssembler
- bin/DistanceEst
- bin/DistanceEst-ssq
- bin/KAligner
- bin/MergeContigs
- bin/MergePaths
- bin/Overlap
- bin/ParseAligns
- bin/PathConsensus
- bin/PathOverlap
- bin/PopBubbles
- bin/SimpleGraph
- bin/abyss-align
- bin/abyss-bloom
- bin/abyss-bloom-dbg
- bin/abyss-bloom-dist.mk
- bin/abyss-bowtie
- bin/abyss-bowtie2
- bin/abyss-bwa
- bin/abyss-bwamem
- bin/abyss-bwasw
- bin/abyss-db-csv
- bin/abyss-db-txt
- bin/abyss-dida
- bin/abyss-fac
- bin/abyss-fatoagp
- bin/abyss-filtergraph
- bin/abyss-fixmate
- bin/abyss-fixmate-ssq
- bin/abyss-gapfill
- bin/abyss-gc
- bin/abyss-index
- bin/abyss-junction
- bin/abyss-kaligner
- bin/abyss-layout
- bin/abyss-longseqdist
- bin/abyss-map
- bin/abyss-map-ssq
- bin/abyss-mergepairs
- bin/abyss-overlap
- bin/abyss-paired-dbg
- bin/abyss-paired-dbg-mpi
- bin/abyss-pe
- bin/abyss-rresolver-short
- bin/abyss-samtoafg
- bin/abyss-scaffold
- bin/abyss-sealer
- bin/abyss-stack-size
- bin/abyss-tabtomd
- bin/abyss-todot
- bin/abyss-tofastq
- bin/konnector
- bin/logcounter
- share/man/man1/abyss-sealer.1.gz
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| bcgsc-abyss-2.3.10_GH0.tar.gz | 1.32349e+06 | 08ff30002113280ae75228eb1e29cf835318c7ef783ccf24fbe7350d49b4043c |
Commit history 0
No commits in the history this site was built from.