BSD Portsbiology/seqan-apps 2.4.0_11 FreeBSD
Official bioinformatic applications based on the SeqAn library
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- h2+[email protected]
- Last update
- Commit
4c7b6443a4- License
- BSD3CLAUSE, LGPL3, GPLv3
- Categories
- biology
- Package size
- 8577.1 KiB, 59578.9 KiB installed
Description
SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data.
This port contains applications built on SeqAn and developed within the SeqAn project. Among them are famous read mappers like RazerS and Yara, as well as many other tools. Some applications are packaged separately and the library can be found at biology/seqan.
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/seqan-apps | 2.4.0_11 |
| DragonFly | biology/seqan-apps | 2.4.0_11 |
Install
Binary package:
pkg install seqan-appsFrom the ports tree:
cd /usr/ports/biology/seqan-apps/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= seqan-apps>0:biology/seqan-appsPackages
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 | 2.4.0_11 | 2.4.0_11 | - | 2.4.0_11 | 2.4.0_11 |
| FreeBSD:14:quarterly | - | - | n/a | 2.4.0_11 | - |
| FreeBSD:15:latest | 2.4.0_11 | 2.4.0_11 | n/a | - | - |
| FreeBSD:15:quarterly | - | - | n/a | n/a | n/a |
| FreeBSD:16:latest | - | 2.4.0_11 | 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 1
boost-libs>0: devel/boost-libs
The full lists below include those, and their dependencies in turn.
Build dependencies 19
No port depends on this one.
Configuration
Options name: biology_seqan-apps
| Option | Default | Description |
|---|---|---|
| AVX2 | off | Use SSE4, AVX2 and POPCNT instructions |
| NATIVE | off | Use all available instruction sets (-march=native) |
| SSE4 | off | Use SSE4 and POPCNT instructions |
- USES
- cmake compiler:c++14-lang
- Service scripts
- none
Files
Manual pages 1
- sak(1)
pkg-plist 160
- bin/alf
- bin/bam2roi
- bin/bed_sort.sh
- bin/bisar
- bin/casbar
- bin/compute_gain
- bin/dfi
- bin/fiona
- bin/four2three
- bin/fx_bam_coverage
- bin/gff_sort.sh
- bin/gustaf
- bin/gustaf_mate_joining
- bin/insegt
- bin/mason_frag_sequencing
- bin/mason_genome
- bin/mason_materializer
- bin/mason_methylation
- bin/mason_simulator
- bin/mason_splicing
- bin/mason_variator
- bin/micro_razers
- bin/pair_align
- bin/param_chooser
- bin/plot.awk
- bin/ps2pswLinks.gawk
- bin/rabema_build_gold_standard
- bin/rabema_evaluate
- bin/rabema_prepare_sam
- bin/razers
- bin/razers3
- bin/rep_sep
- bin/roi_feature_projection
- bin/roi_plot_9.sh
- bin/roi_plot_thumbnails
- bin/roi_sort.sh
- bin/s4_join
- bin/s4_search
- bin/sak
- bin/sam2matrix
- bin/samcat
- bin/seqan_tcoffee
- bin/seqcons2
- bin/sgip
- bin/snp_store
- bin/splazers
- bin/stellar
- bin/tree_recon
- bin/yara_indexer
- bin/yara_mapper
- share/man/man1/sak.1.gz
- share/doc/alf/LICENSE
- share/doc/alf/README
- share/doc/alf/example/small.fasta
- share/doc/bs_tools/LICENSE
- share/doc/bs_tools/README
- share/doc/dfi/LICENSE
- share/doc/dfi/README
- share/doc/dfi/example/fasta1.fa
- share/doc/dfi/example/fasta2.fa
- share/doc/fiona/LICENSE
- share/doc/fiona/README
- share/doc/fiona/example/reads.fa
- share/doc/fx_tools/LICENSE
- share/doc/fx_tools/README
- share/doc/gustaf/LICENSE
- share/doc/gustaf/README
- share/doc/gustaf/example/adeno.fa
- share/doc/gustaf/example/adeno_modified.fa
- share/doc/gustaf/example/adeno_modified_reads.fa
- share/doc/gustaf/example/stellar.gff
- share/doc/insegt/LICENSE
- share/doc/insegt/README
- share/doc/insegt/example/annoOutput.gff
- share/doc/insegt/example/annotations.gff
- share/doc/insegt/example/readOutput.gff
- share/doc/insegt/example/tupleOutput.gff
- share/doc/mason2/LICENSE
- share/doc/mason2/README
- share/doc/mason2/README.mason_frag_sequencing
- share/doc/mason2/README.mason_genome
- share/doc/mason2/README.mason_materializer
- share/doc/mason2/README.mason_methylation
- share/doc/mason2/README.mason_simulator
- share/doc/mason2/README.mason_splicing
- share/doc/mason2/README.mason_variator
- share/doc/mason2/example/adeno_virus.fa
- share/doc/micro_razers/LICENSE
- share/doc/micro_razers/README
- share/doc/micro_razers/example/genome.fa
- share/doc/micro_razers/example/reads.fa
- share/doc/micro_razers/example/reads.fa.result
- share/doc/ngs_roi/LICENSE
- share/doc/ngs_roi/R/ngsroi_0.1.tar.gz
- share/doc/ngs_roi/R/ngsroi_0.1.zip
- share/doc/ngs_roi/README
- share/doc/ngs_roi/example/dmel.bed
- share/doc/ngs_roi/example/dmel.gtf
- share/doc/ngs_roi/example/example.bam
- share/doc/pair_align/LICENSE
The first 100 are listed.
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| seqan-seqan-seqan-v2.4.0_GH0.tar.gz | 1.09626901e+08 | d7084d17729214003e84818e0280a16f223c8f1c6a30eeef040c27e0c0047bd7 |