BSD Portsbiology/gmap 2025.07.31_1 FreeBSD
Genomic Mapping and Alignment Program for mRNA and EST Sequences
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
3e5b7601e1- License
- GMAP
- Categories
- biology
- Package size
- 5790.1 KiB, 40885.4 KiB installed
Description
A standalone program for mapping and aligning cDNA sequences to a genome. The program maps and aligns a single sequence with minimal startup time and memory requirements, and provides fast batch processing of large sequence sets. The program generates accurate gene structures, even in the presence of substantial polymorphisms and sequence errors, without using probabilistic splice site models. Methodology underlying the program includes a minimal sampling strategy for genomic mapping, oligomer chaining for approximate alignment, sandwich DP for splice site detection, and microexon identification with statistical significance testing.
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/gmap | 2025.07.31_1 |
| DragonFly | biology/gmap | 2020.09.12 |
Install
Binary package:
pkg install gmapFrom the ports tree:
cd /usr/ports/biology/gmap/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= gmap>0:biology/gmapPackages
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 | 2025.07.31_1 | 2025.07.31_1 | - | - | 2025.07.31_1 |
| FreeBSD:14:quarterly | - | 2025.07.31 | n/a | - | 2025.07.31 |
| FreeBSD:15:latest | 2025.07.31_1 | 2025.07.31_1 | n/a | - | 2020.09.12 |
| FreeBSD:15:quarterly | - | 2025.07.31 | n/a | n/a | n/a |
| FreeBSD:16:latest | - | 2025.07.31_1 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependencies
The Makefile names none itself; they come from USES and USE_*.
The full lists below include those, and their dependencies in turn.
Build dependencies 4
Run dependencies 1
No port depends on this one.
Configuration
Options name: biology_gmap
| Option | Default | Description |
|---|---|---|
| SIMD | off | Use CPU-specific optimizations |
- USES
- gmake perl5
- Service scripts
- none
- Conflicts with
- cpuid scotch
Message after installing
The default configuration for the gmap port disables all optimizations to maintain compatibility with the widest range of systems. To get a binary optimized for your system please deinstall gmap and build from ports using "make config" to enable the SIMD option. ===> NOTICE: The gmap port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing
Files
pkg-plist 40
- bin/atoiindex
- bin/cmetindex
- bin/cpuid
- bin/dbsnp_iit
- bin/ensembl_genes
- bin/fa_coords
- bin/get-genome
- bin/gff3_exons
- bin/gff3_genes
- bin/gff3_introns
- bin/gff3_splicesites
- bin/gmap
- bin/gmap.nosimd
- bin/gmap_build
- bin/gmap_cat
- bin/gmap_process
- bin/gmapindex
- bin/gmapl
- bin/gmapl.nosimd
- bin/gsnap
- bin/gsnap.nosimd
- bin/gsnapl
- bin/gsnapl.nosimd
- bin/gtf_exons
- bin/gtf_genes
- bin/gtf_introns
- bin/gtf_splicesites
- bin/gtf_transcript_splicesites
- bin/gvf_iit
- bin/iit_dump
- bin/iit_get
- bin/iit_store
- bin/indexdb_cat
- bin/md_coords
- bin/psl_genes
- bin/psl_introns
- bin/psl_splicesites
- bin/snpindex
- bin/trindex
- bin/vcf_iit
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| gmap-gsnap-2025-07-31.tar.gz | 5.231678e+06 | cc7212446683785a5b94aba79861212360d421ea409cd7cbf287f1dc63ed844d |
Master sites 1
- http://research-pub.gene.com/gmap/src/