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Port details
samtools Tools for manipulating next-generation sequencing data
1.13 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 1.13Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2014-12-15 21:59:37
Last Update: 2021-07-12 13:24:26
Commit Hash: 1c1b494
License: MIT
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (64 items)
Collapse this list.
  1. /usr/local/share/licenses/samtools-1.13/catalog.mk
  2. /usr/local/share/licenses/samtools-1.13/LICENSE
  3. /usr/local/share/licenses/samtools-1.13/MIT
  4. bin/ace2sam
  5. bin/blast2sam.pl
  6. bin/bowtie2sam.pl
  7. bin/export2sam.pl
  8. bin/fasta-sanitize.pl
  9. bin/interpolate_sam.pl
  10. bin/maq2sam-long
  11. bin/maq2sam-short
  12. bin/md5fa
  13. bin/md5sum-lite
  14. bin/novo2sam.pl
  15. bin/plot-ampliconstats
  16. bin/plot-bamstats
  17. bin/psl2sam.pl
  18. bin/sam2vcf.pl
  19. bin/samtools
  20. bin/samtools.pl
  21. bin/seq_cache_populate.pl
  22. bin/soap2sam.pl
  23. bin/wgsim
  24. bin/wgsim_eval.pl
  25. bin/zoom2sam.pl
  26. man/man1/samtools-addreplacerg.1.gz
  27. man/man1/samtools-ampliconclip.1.gz
  28. man/man1/samtools-ampliconstats.1.gz
  29. man/man1/samtools-bedcov.1.gz
  30. man/man1/samtools-calmd.1.gz
  31. man/man1/samtools-cat.1.gz
  32. man/man1/samtools-collate.1.gz
  33. man/man1/samtools-coverage.1.gz
  34. man/man1/samtools-depad.1.gz
  35. man/man1/samtools-depth.1.gz
  36. man/man1/samtools-dict.1.gz
  37. man/man1/samtools-faidx.1.gz
  38. man/man1/samtools-fasta.1.gz
  39. man/man1/samtools-fastq.1.gz
  40. man/man1/samtools-fixmate.1.gz
  41. man/man1/samtools-flags.1.gz
  42. man/man1/samtools-flagstat.1.gz
  43. man/man1/samtools-fqidx.1.gz
  44. man/man1/samtools-idxstats.1.gz
  45. man/man1/samtools-import.1.gz
  46. man/man1/samtools-index.1.gz
  47. man/man1/samtools-markdup.1.gz
  48. man/man1/samtools-merge.1.gz
  49. man/man1/samtools-mpileup.1.gz
  50. man/man1/samtools-phase.1.gz
  51. man/man1/samtools-quickcheck.1.gz
  52. man/man1/samtools-reheader.1.gz
  53. man/man1/samtools-rmdup.1.gz
  54. man/man1/samtools-sort.1.gz
  55. man/man1/samtools-split.1.gz
  56. man/man1/samtools-stats.1.gz
  57. man/man1/samtools-targetcut.1.gz
  58. man/man1/samtools-tview.1.gz
  59. man/man1/samtools-view.1.gz
  60. man/man1/samtools.1.gz
  61. man/man1/wgsim.1.gz
  62. @owner
  63. @group
  64. @mode
Collapse this list.
Dependency lines:
  • samtools>0:biology/samtools
To install the port:
cd /usr/ports/biology/samtools/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/samtools
  • pkg install samtools
PKGNAME: samtools
Flavors: there is no flavor information for this port.
distinfo:
Packages (timestamps in pop-ups are UTC):
samtools
ABIlatestquarterly
FreeBSD:11:aarch641.91.9
FreeBSD:11:amd641.131.12
FreeBSD:11:armv61.3.11.9
FreeBSD:11:i3861.131.12
FreeBSD:11:mips--
FreeBSD:11:mips641.3.1-
FreeBSD:12:aarch641.91.13
FreeBSD:12:amd641.131.13
FreeBSD:12:armv61.91.10
FreeBSD:12:armv71.91.10
FreeBSD:12:i3861.131.13
FreeBSD:12:mips--
FreeBSD:12:mips641.9-
FreeBSD:12:powerpc64-1.12
FreeBSD:13:aarch641.111.13
FreeBSD:13:amd641.131.13
FreeBSD:13:armv61.111.12
FreeBSD:13:armv71.111.13
FreeBSD:13:i3861.131.13
FreeBSD:13:mips--
FreeBSD:13:mips641.111.11
FreeBSD:13:powerpc641.111.12
FreeBSD:14:aarch641.13-
FreeBSD:14:amd641.13-
FreeBSD:14:armv61.12-
FreeBSD:14:armv71.12-
FreeBSD:14:i3861.13-
FreeBSD:14:mips--
FreeBSD:14:mips641.13-
FreeBSD:14:powerpc641.12-
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake>=4.3 : devel/gmake
  2. autoconf>=2.69 : devel/autoconf
  3. automake>=1.16.1 : devel/automake
Library dependencies:
  1. libhts.so : biology/htslib
This port is required by:
for Run
  1. biology/biostar-tools
  2. biology/ddocent
  3. biology/picard-tools

Configuration Options:
Options name:

USES:

FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/samtools/samtools/tar.gz/1.13?dummy=/
Collapse this list.

Number of commits found: 18

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
12 Jul 2021 13:24:26
 files touched by this commit commit hash:1c1b4943aef7525da9e15fb8f419c08e2f8849bf  1.13
Jason W. Bacon (jwb) search for other commits by this committer
biology/samtools: Update to 1.13

Numerous enhancements and bug fixes

Changes:        https://github.com/samtools/samtools/releases/tag/1.13
06 Apr 2021 14:31:07
 files touched by this commit commit hash:305f148f482daf30dcf728039d03d019f88344eb  1.12
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
20 Mar 2021 17:14:32
Original commit files touched by this commit Revision:568874  1.12
jwb search for other commits by this committer
biology/htslib: Update to 1.12
biology/samtools: Update to 1.12
biology/bcftools: Update to 1.12

Numerous enhancements, performance improvements, and bug fixes since 1.11

Build-tested all other htslib dependents, no revbumps should be needed

Reported by:    portscout
05 Nov 2020 20:32:40
Original commit files touched by this commit Revision:554156  1.11
jwb search for other commits by this committer
biology/samtools: Upgrade to 1.11

Numerous new features, bug fixes and performance enhancements
https://github.com/samtools/samtools/releases/tag/1.11

Reported by:    portscout
03 Aug 2020 18:22:06
Original commit files touched by this commit Revision:544098  1.10
jwb search for other commits by this committer
biology/samtools: Upgrade to 1.10

Numerous bug fixes and enhancements:
https://github.com/samtools/samtools/releases/tag/1.10

Take maintainership per ports/248089

PR:             ports/248089
03 Aug 2020 17:40:04
Original commit files touched by this commit Revision:544090  1.9_1
jwb search for other commits by this committer
biology/htslib: Upgrade to 1.10.2

Numerous bug fixes and enhancements since 1.9:
https://github.com/samtools/htslib/tags

Bump PORTREVISION on dependents that don't require additional patching

PR:             248089
13 Aug 2019 16:00:39
Original commit files touched by this commit Revision:508834  1.9
mat search for other commits by this committer
Convert to UCL & cleanup pkg-message (categories a-c)
02 Aug 2018 19:28:36
Original commit files touched by this commit Revision:476246  1.9
fernape search for other commits by this committer
biology/samtools: update to 1.9

PR:	230171
Submitted by:	ndowens.fbsd@yandex.com
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D16569
04 Dec 2017 15:27:29
Refresh Original commit files touched by this commit Revision:455518  Sanity Test Failure
mat search for other commits by this committer
Add a USES=python:env, that will not add a dependency on Python.

It has the same effect than setting PYTHON_NO_DEPENDS, but in a more
compact way.

Sponsored by:	Absolight
25 Oct 2017 10:19:50
Original commit files touched by this commit Revision:452840  1.6
pizzamig search for other commits by this committer
biology/htslib biology/bcftools biology/samtools: Update to 1.6

PR:		223094
Submitted by:	mzaki@niid.go.jp
Approved by:	cartwright@asu.edu (maintainer)
Approved by:	olivier (mentor)
Differential Revision:	https://reviews.freebsd.org/D12768
26 May 2016 20:28:55
Original commit files touched by this commit Revision:415914  1.3.1
pi search for other commits by this committer
biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1

Changes:
  https://sourceforge.net/p/samtools/mailman/message/35033807/

PR:		209653
Submitted by:	cartwright@asu.edu (maintainer)
19 May 2016 11:09:14
Original commit files touched by this commit Revision:415503  1.3
amdmi3 search for other commits by this committer
- Fix trailing whitespace in pkg-messages

Approved by:	portmgr blanket
01 Apr 2016 13:29:17
Original commit files touched by this commit Revision:412344  1.3
mat search for other commits by this committer
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
01 Feb 2016 21:59:15
Original commit files touched by this commit Revision:407776  1.3
marino search for other commits by this committer
biology/samtools: document ncurses requirement (USES+=ncurses)

approved by:	infrastructure blanket
25 Dec 2015 01:31:09
Original commit files touched by this commit Revision:404398  1.3
junovitch search for other commits by this committer
biology/{bcftools,htslib,samtools}: update 1.2.x -> 1.3

- Update ports to 1.3 and set BUILD_DEPENDS of dependent ports to require
  version 1.3 of htslib.
- Add CURL option to htslib
- Add TEST_TARGET with perl and bash dependencies for testing
- Tidy up spacing and pkg-message's

PR:		205524
PR:		205525
PR:		205526
Submitted by:	cartwright@asu.edu (maintainer)
06 May 2015 15:16:54
Original commit files touched by this commit Revision:385521  1.2
mat search for other commits by this committer
Update ports in the [bcd]* categories to not use GH_COMMIT.

With minor cleanups to make things simpler.

With hat:	portmgr
Sponsored by:	Absolight
06 Mar 2015 12:53:59
Original commit files touched by this commit Revision:380597  1.2
robak search for other commits by this committer
biology/samtools: update 1.1 -> 1.2

PR:		198292
Submitted by:	Reed Cartwright <cartwright@asu.edu>
15 Dec 2014 21:59:20
Original commit files touched by this commit Revision:374767  1.1
pawel search for other commits by this committer
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.

WWW: http://www.htslib.org/

PR:		195592
Submitted by:	Reed A. Cartwright <cartwright@asu.edu>

Number of commits found: 18