notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)
Want a good monitor light? See my photosAll times are UTC
Ukraine
This referral link gives you 10% off a Fastmail.com account and gives me a discount on my Fastmail account.

Get notified when packages are built

A new feature has been added. FreshPorts already tracks package built by the FreeBSD project. This information is displayed on each port page. You can now get an email when FreshPorts notices a new package is available for something on one of your watch lists. However, you must opt into that. Click on Report Subscriptions on the right, and New Package Notification box, and click on Update.

Finally, under Watch Lists, click on ABI Package Subscriptions to select your ABI (e.g. FreeBSD:14:amd64) & package set (latest/quarterly) combination for a given watch list. This is what FreshPorts will look for.

Port details
samtools Tools for manipulating next-generation sequencing data
1.17_1 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 1.17Version 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: 2024-03-02 19:40:58
Commit Hash: 01064ce
License: MIT
WWW:
https://www.htslib.org/
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.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (70 items)
Collapse this list.
  1. /usr/local/share/licenses/samtools-1.17_1/catalog.mk
  2. /usr/local/share/licenses/samtools-1.17_1/LICENSE
  3. /usr/local/share/licenses/samtools-1.17_1/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. share/man/man1/samtools-addreplacerg.1.gz
  27. share/man/man1/samtools-ampliconclip.1.gz
  28. share/man/man1/samtools-ampliconstats.1.gz
  29. share/man/man1/samtools-bedcov.1.gz
  30. share/man/man1/samtools-calmd.1.gz
  31. share/man/man1/samtools-cat.1.gz
  32. share/man/man1/samtools-collate.1.gz
  33. share/man/man1/samtools-consensus.1.gz
  34. share/man/man1/samtools-coverage.1.gz
  35. share/man/man1/samtools-cram-size.1.gz
  36. share/man/man1/samtools-depad.1.gz
  37. share/man/man1/samtools-depth.1.gz
  38. share/man/man1/samtools-dict.1.gz
  39. share/man/man1/samtools-faidx.1.gz
  40. share/man/man1/samtools-fasta.1.gz
  41. share/man/man1/samtools-fastq.1.gz
  42. share/man/man1/samtools-fixmate.1.gz
  43. share/man/man1/samtools-flags.1.gz
  44. share/man/man1/samtools-flagstat.1.gz
  45. share/man/man1/samtools-fqidx.1.gz
  46. share/man/man1/samtools-head.1.gz
  47. share/man/man1/samtools-idxstats.1.gz
  48. share/man/man1/samtools-import.1.gz
  49. share/man/man1/samtools-index.1.gz
  50. share/man/man1/samtools-markdup.1.gz
  51. share/man/man1/samtools-merge.1.gz
  52. share/man/man1/samtools-mpileup.1.gz
  53. share/man/man1/samtools-phase.1.gz
  54. share/man/man1/samtools-quickcheck.1.gz
  55. share/man/man1/samtools-reference.1.gz
  56. share/man/man1/samtools-reheader.1.gz
  57. share/man/man1/samtools-reset.1.gz
  58. share/man/man1/samtools-rmdup.1.gz
  59. share/man/man1/samtools-samples.1.gz
  60. share/man/man1/samtools-sort.1.gz
  61. share/man/man1/samtools-split.1.gz
  62. share/man/man1/samtools-stats.1.gz
  63. share/man/man1/samtools-targetcut.1.gz
  64. share/man/man1/samtools-tview.1.gz
  65. share/man/man1/samtools-view.1.gz
  66. share/man/man1/samtools.1.gz
  67. share/man/man1/wgsim.1.gz
  68. @owner
  69. @group
  70. @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
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: samtools
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1677245969 SHA256 (samtools-samtools-1.17_GH0.tar.gz) = f76ec1880468ecaa5341a7256ae896f2cfb191193dbb683046776fb81e18af49 SIZE (samtools-samtools-1.17_GH0.tar.gz) = 5459752

Packages (timestamps in pop-ups are UTC):
samtools
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest1.17_11.17_11.111.17_11.17_1-1.11-
FreeBSD:13:quarterly1.171.171.171.171.171.171.171.17
FreeBSD:14:latest1.17_11.17_11.16.11.171.17_11.17-1.17
FreeBSD:14:quarterly1.171.17-1.171.171.171.171.17
FreeBSD:15:latest1.17_11.17_1n/a1.17n/a1.171.171.17
FreeBSD:15:quarterly--n/a-n/a---
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>=2.71 : devel/autoconf
  3. automake>=1.16.5 : devel/automake
Test dependencies:
  1. bash : shells/bash
  2. perl5>=5.36<5.37 : lang/perl5.36
Library dependencies:
  1. libhts.so : biology/htslib
This port is required by:
for Build
  1. biology/btllib
for Run
  1. biology/atac-seq
  2. biology/augustus
  3. biology/biostar-tools
  4. biology/btllib
  5. biology/chip-seq
  6. biology/ddocent
  7. biology/picard-tools
Expand this list (8 items / 1 hidden - sorry, this count includes any deleted ports)
  1. Collapse this list).
  2. biology/rna-seq
  3. Collapse this list.

Configuration Options:
No options to configure
Options name:
biology_samtools
USES:
autoreconf gmake localbase ncurses perl5 python:env shebangfix
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/1.17?dummy=/
Collapse this list.

Number of commits found: 26

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
1.17_1
02 Mar 2024 19:40:58
commit hash: 01064ce0bda11469f31eaabb93e6c1eefa968661commit hash: 01064ce0bda11469f31eaabb93e6c1eefa968661commit hash: 01064ce0bda11469f31eaabb93e6c1eefa968661commit hash: 01064ce0bda11469f31eaabb93e6c1eefa968661 files touched by this commit
Nuno Teixeira (eduardo) search for other commits by this committer
biology/samtools: Move man pages to share/man

Approved by:	portmgr (blanket)
1.17
24 Feb 2023 23:27:21
commit hash: 1993bfc7cf7d933c1a8cc11bf2198ce8691a0d76commit hash: 1993bfc7cf7d933c1a8cc11bf2198ce8691a0d76commit hash: 1993bfc7cf7d933c1a8cc11bf2198ce8691a0d76commit hash: 1993bfc7cf7d933c1a8cc11bf2198ce8691a0d76 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/samtools: Update to 1.17

Numerous enhancements and bug fixes

Changes: https://github.com/samtools/samtools/releases

Reported by:    portscout
1.16.1
05 Jan 2023 23:17:34
commit hash: 193567cc9e20e9ecb305506d92f522fc77dd18e4commit hash: 193567cc9e20e9ecb305506d92f522fc77dd18e4commit hash: 193567cc9e20e9ecb305506d92f522fc77dd18e4commit hash: 193567cc9e20e9ecb305506d92f522fc77dd18e4 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/samtools: Update to 1.16.1

New "reference" subcommand to extract CRAM features (1.16)
Numerous minor enhancements and bug fixes

Changes: https://github.com/samtools/samtools/releases
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
1.15
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
1.15
20 Jul 2022 14:20:57
commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 files touched by this commit
Tobias C. Berner (tcberner) search for other commits by this committer
biology: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Akinori MUSHA aka knu <knu@idaemons.org>
  *  Andrey Zakhvatov
  *  Bob Zimmermann <rpz@cse.wustl.edu>
  *  Camson Huynh <chuynh@biolateral.com.au>
  *  Dan Siercks <dsiercks@uwm.edu>
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Hannes Hauswedell <h2+fbsdports@fsfe.org>
  *  J. Bacon <jwb@FreeBSD.org>
  *  Jason Bacon <jwb@FreeBSD.org>
  *  Jeremy <karlj000@unbc.ca>
(Only the first 15 lines of the commit message are shown above View all of this commit message)
1.15
26 Feb 2022 15:04:10
commit hash: 822ec7476b36d4a004c88067044432fbc29ca9f4commit hash: 822ec7476b36d4a004c88067044432fbc29ca9f4commit hash: 822ec7476b36d4a004c88067044432fbc29ca9f4commit hash: 822ec7476b36d4a004c88067044432fbc29ca9f4 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/samtools: Update to 1.15

Several small enhancements and a few bug fixes
Changes: https://github.com/samtools/samtools/releases

Reported by:    portscout
1.14
18 Dec 2021 17:56:51
commit hash: d0228a8a5f1c2b80211af892f32847ff4edb241fcommit hash: d0228a8a5f1c2b80211af892f32847ff4edb241fcommit hash: d0228a8a5f1c2b80211af892f32847ff4edb241fcommit hash: d0228a8a5f1c2b80211af892f32847ff4edb241f files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/samtools: Update to 1.14

Several enhancements and minor bug fixes

Changes: https://github.com/samtools/samtools/tags
1.13
12 Jul 2021 13:24:26
commit hash: 1c1b4943aef7525da9e15fb8f419c08e2f8849bfcommit hash: 1c1b4943aef7525da9e15fb8f419c08e2f8849bfcommit hash: 1c1b4943aef7525da9e15fb8f419c08e2f8849bfcommit hash: 1c1b4943aef7525da9e15fb8f419c08e2f8849bf files touched by this commit
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
1.12
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
1.12
20 Mar 2021 17:14:32
Revision:568874Original commit files touched by this commit
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
1.11
05 Nov 2020 20:32:40
Revision:554156Original commit files touched by this commit
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
1.10
03 Aug 2020 18:22:06
Revision:544098Original commit files touched by this commit
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
1.9_1
03 Aug 2020 17:40:04
Revision:544090Original commit files touched by this commit
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
1.9
13 Aug 2019 16:00:39
Revision:508834Original commit files touched by this commit
mat search for other commits by this committer
Convert to UCL & cleanup pkg-message (categories a-c)
1.9
02 Aug 2018 19:28:36
Revision:476246Original commit files touched by this commit
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
Revision:455518Original commit files touched by this commit Sanity Test Failure Refresh
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
1.6
25 Oct 2017 10:19:50
Revision:452840Original commit files touched by this commit
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
1.3.1
26 May 2016 20:28:55
Revision:415914Original commit files touched by this commit
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)
1.3
19 May 2016 11:09:14
Revision:415503Original commit files touched by this commit
amdmi3 search for other commits by this committer
- Fix trailing whitespace in pkg-messages

Approved by:	portmgr blanket
1.3
01 Apr 2016 13:29:17
Revision:412344Original commit files touched by this commit
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
1.3
01 Feb 2016 21:59:15
Revision:407776Original commit files touched by this commit
marino search for other commits by this committer
biology/samtools: document ncurses requirement (USES+=ncurses)

approved by:	infrastructure blanket
1.3
25 Dec 2015 01:31:09
Revision:404398Original commit files touched by this commit
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)
1.2
06 May 2015 15:16:54
Revision:385521Original commit files touched by this commit
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
1.2
06 Mar 2015 12:53:59
Revision:380597Original commit files touched by this commit
robak search for other commits by this committer
biology/samtools: update 1.1 -> 1.2

PR:		198292
Submitted by:	Reed Cartwright <cartwright@asu.edu>
1.1
15 Dec 2014 21:59:20
Revision:374767Original commit files touched by this commit
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: 26