biology/samtools 1.24 FreeBSD
Tools for manipulating next-generation sequencing data
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
2414383046- License
- MIT
- Categories
- biology
- Package size
- 515.4 KiB, 1150.8 KiB installed
Description
Samtools implements various utilities for post-processing alignments in the SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer.
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/samtools | 1.24 |
| NetBSD | biology/samtools | 1.21 |
| DragonFly | biology/samtools | 1.21 |
Install
Binary package:
pkg install samtoolsFrom the ports tree:
cd /usr/ports/biology/samtools/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= samtools>0:biology/samtoolsPackages
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 | 1.24 | 1.24 | 1.16.1 | - | 1.24 |
| FreeBSD:14:quarterly | 1.24 | 1.24 | n/a | - | 1.24 |
| FreeBSD:15:latest | 1.24 | 1.24 | n/a | - | 1.22 |
| FreeBSD:15:quarterly | 1.24 | 1.24 | n/a | n/a | n/a |
| FreeBSD:16:latest | 1.24 | 1.24 | 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
htslib>=1.24: biology/htslib
Library 1
libhts.so: biology/htslib
Test 1
bash: shells/bash
The full lists below include those, and their dependencies in turn.
Build dependencies 19
Run dependencies 12
Configuration
No options to configure.
- USES
- autoreconf cpe gmake localbase ncurses perl5 python:env shebangfix
- Service scripts
- none
Message after installing
===> NOTICE: The samtools 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
Manual pages 43
- samtools(1)
- samtools-addreplacerg(1)
- samtools-ampliconclip(1)
- samtools-ampliconstats(1)
- samtools-bedcov(1)
- samtools-calmd(1)
- samtools-cat(1)
- samtools-checksum(1)
- samtools-collate(1)
- samtools-consensus(1)
- samtools-coverage(1)
- samtools-cram-size(1)
- samtools-depad(1)
- samtools-depth(1)
- samtools-dict(1)
- samtools-faidx(1)
- samtools-fasta(1)
- samtools-fastq(1)
- samtools-fixmate(1)
- samtools-flags(1)
- samtools-flagstat(1)
- samtools-fqidx(1)
- samtools-head(1)
- samtools-idxstats(1)
- samtools-import(1)
- samtools-index(1)
- samtools-markdup(1)
- samtools-merge(1)
- samtools-mpileup(1)
- samtools-phase(1)
- samtools-quickcheck(1)
- samtools-reference(1)
- samtools-reheader(1)
- samtools-reset(1)
- samtools-rmdup(1)
- samtools-samples(1)
- samtools-sort(1)
- samtools-split(1)
- samtools-stats(1)
- samtools-targetcut(1)
- samtools-tview(1)
- samtools-view(1)
- wgsim(1)
pkg-plist 66
- bin/ace2sam
- bin/blast2sam.pl
- bin/bowtie2sam.pl
- bin/export2sam.pl
- bin/fasta-sanitize.pl
- bin/interpolate_sam.pl
- bin/maq2sam-long
- bin/maq2sam-short
- bin/md5fa
- bin/md5sum-lite
- bin/novo2sam.pl
- bin/plot-ampliconstats
- bin/plot-bamstats
- bin/psl2sam.pl
- bin/sam2vcf.pl
- bin/samtools
- bin/samtools.pl
- bin/seq_cache_populate.pl
- bin/seq_cache_populate.py
- bin/soap2sam.pl
- bin/wgsim
- bin/wgsim_eval.pl
- bin/zoom2sam.pl
- share/man/man1/samtools-addreplacerg.1.gz
- share/man/man1/samtools-ampliconclip.1.gz
- share/man/man1/samtools-ampliconstats.1.gz
- share/man/man1/samtools-bedcov.1.gz
- share/man/man1/samtools-calmd.1.gz
- share/man/man1/samtools-cat.1.gz
- share/man/man1/samtools-checksum.1.gz
- share/man/man1/samtools-collate.1.gz
- share/man/man1/samtools-consensus.1.gz
- share/man/man1/samtools-coverage.1.gz
- share/man/man1/samtools-cram-size.1.gz
- share/man/man1/samtools-depad.1.gz
- share/man/man1/samtools-depth.1.gz
- share/man/man1/samtools-dict.1.gz
- share/man/man1/samtools-faidx.1.gz
- share/man/man1/samtools-fasta.1.gz
- share/man/man1/samtools-fastq.1.gz
- share/man/man1/samtools-fixmate.1.gz
- share/man/man1/samtools-flags.1.gz
- share/man/man1/samtools-flagstat.1.gz
- share/man/man1/samtools-fqidx.1.gz
- share/man/man1/samtools-head.1.gz
- share/man/man1/samtools-idxstats.1.gz
- share/man/man1/samtools-import.1.gz
- share/man/man1/samtools-index.1.gz
- share/man/man1/samtools-markdup.1.gz
- share/man/man1/samtools-merge.1.gz
- share/man/man1/samtools-mpileup.1.gz
- share/man/man1/samtools-phase.1.gz
- share/man/man1/samtools-quickcheck.1.gz
- share/man/man1/samtools-reference.1.gz
- share/man/man1/samtools-reheader.1.gz
- share/man/man1/samtools-reset.1.gz
- share/man/man1/samtools-rmdup.1.gz
- share/man/man1/samtools-samples.1.gz
- share/man/man1/samtools-sort.1.gz
- share/man/man1/samtools-split.1.gz
- share/man/man1/samtools-stats.1.gz
- share/man/man1/samtools-targetcut.1.gz
- share/man/man1/samtools-tview.1.gz
- share/man/man1/samtools-view.1.gz
- share/man/man1/samtools.1.gz
- share/man/man1/wgsim.1.gz
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| samtools-samtools-1.24_GH0.tar.gz | 5.77614e+06 | 46be6a9c9dc593981d699fb8efa46977faf45160b34c0b29749b35e394c6b61d |