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Port details
bcftools Tools for manipulating next-generation sequencing data
1.11 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 1.11Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2015-06-05 21:01:24
Last Update: 2020-11-05 20:34:04
SVN Revision: 554157
License: MIT GPLv3
Description:
SVNWeb : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (55 items)
Collapse this list.
  1. @ldconfig
  2. /usr/local/share/licenses/bcftools-1.11/catalog.mk
  3. /usr/local/share/licenses/bcftools-1.11/LICENSE
  4. /usr/local/share/licenses/bcftools-1.11/MIT
  5. /usr/local/share/licenses/bcftools-1.11/GPLv3
  6. bin/bcftools
  7. bin/color-chrs
  8. bin/gff2gff.py
  9. bin/guess-ploidy
  10. bin/plot-roh
  11. bin/plot-vcfstats
  12. bin/run-roh
  13. bin/vcfutils
  14. libexec/bcftools/GTisec.so
  15. libexec/bcftools/GTsubset.so
  16. libexec/bcftools/ad-bias.so
  17. libexec/bcftools/add-variantkey.so
  18. libexec/bcftools/af-dist.so
  19. libexec/bcftools/allele-length.so
  20. libexec/bcftools/check-ploidy.so
  21. libexec/bcftools/check-sparsity.so
  22. libexec/bcftools/color-chrs.so
  23. libexec/bcftools/contrast.so
  24. libexec/bcftools/counts.so
  25. libexec/bcftools/dosage.so
  26. libexec/bcftools/fill-AN-AC.so
  27. libexec/bcftools/fill-from-fasta.so
  28. libexec/bcftools/fill-tags.so
  29. libexec/bcftools/fixploidy.so
  30. libexec/bcftools/fixref.so
  31. libexec/bcftools/frameshifts.so
  32. libexec/bcftools/guess-ploidy.so
  33. libexec/bcftools/gvcfz.so
  34. libexec/bcftools/impute-info.so
  35. libexec/bcftools/indel-stats.so
  36. libexec/bcftools/isecGT.so
  37. libexec/bcftools/mendelian.so
  38. libexec/bcftools/missing2ref.so
  39. libexec/bcftools/parental-origin.so
  40. libexec/bcftools/prune.so
  41. libexec/bcftools/remove-overlaps.so
  42. libexec/bcftools/scatter.so
  43. libexec/bcftools/setGT.so
  44. libexec/bcftools/smpl-stats.so
  45. libexec/bcftools/split-vep.so
  46. libexec/bcftools/split.so
  47. libexec/bcftools/tag2tag.so
  48. libexec/bcftools/trio-dnm.so
  49. libexec/bcftools/trio-stats.so
  50. libexec/bcftools/trio-switch-rate.so
  51. libexec/bcftools/variantkey-hex.so
  52. man/man1/bcftools.1.gz
  53. @owner
  54. @group
  55. @mode
Collapse this list.
Dependency lines:
  • ${PYTHON_PKGNAMEPREFIX}>0:biology/bcftools@${PY_FLAVOR}
To install the port: cd /usr/ports/biology/bcftools/ && make install clean
To add the package: pkg install bcftools
PKGNAME: bcftools
Flavors: there is no flavor information for this port.
distinfo:
Packages: (move your mouse over the cells for more information)
bcftools
ABIlatestquarterly
FreeBSD:11:aarch641.91.9_1
FreeBSD:11:amd641.111.11
FreeBSD:11:armv61.3.11.9_1
FreeBSD:11:i3861.111.11
FreeBSD:11:mips1.3.1-
FreeBSD:11:mips641.3.1-
FreeBSD:12:aarch641.91.11
FreeBSD:12:amd641.111.11
FreeBSD:12:armv61.91.10.2
FreeBSD:12:armv71.91.10.2
FreeBSD:12:i3861.111.11
FreeBSD:12:mips1.9-
FreeBSD:12:mips641.9-
FreeBSD:12:powerpc64-1.11
FreeBSD:13:aarch641.111.11
FreeBSD:13:amd641.111.11
FreeBSD:13:armv61.111.11
FreeBSD:13:armv71.111.11
FreeBSD:13:i3861.111.11
FreeBSD:13:mips--
FreeBSD:13:mips641.111.11
FreeBSD:13:powerpc641.111.11
FreeBSD:14:aarch641.11-
FreeBSD:14:amd641.11-
FreeBSD:14:armv61.11-
FreeBSD:14:armv71.11-
FreeBSD:14:i3861.11-
FreeBSD:14:mips--
FreeBSD:14:mips641.11-
FreeBSD:14:powerpc641.11-
 

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
Runtime dependencies:
  1. bash : shells/bash
Library dependencies:
  1. libhts.so.3 : biology/htslib
  2. libgsl.so : math/gsl
There are no ports dependent upon this port

Configuration Options

USES:

Master Sites:
Expand this list (1 items)
    Collapse this list.
  1. https://codeload.github.com/samtools/bcftools/tar.gz/1.11?dummy=/
  2. Collapse this list.

Number of commits found: 16

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
05 Nov 2020 20:34:04
Original commit files touched by this commit  1.11
Revision:554157
jwb search for other commits by this committer
biology/bcftools: Upgrade to 1.11

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

Reported by:    portscout
03 Aug 2020 18:16:54
Original commit files touched by this commit  1.10.2
Revision:544096
jwb search for other commits by this committer
biology/bcftools: Upgrade to 1.10.2

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

Take maintainership per ports/248089.

PR:             ports/248089
03 Aug 2020 17:40:04
Original commit files touched by this commit  1.9_2
Revision:544090
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
25 Oct 2019 23:41:34
Original commit files touched by this commit  1.9_1
Revision:515671
tcberner search for other commits by this committer
math/gsl: update to 2.6

- math/p5-Math-GSL does not seem to have any upstream activity to make it work
with this version -> mark it broken
  - this also breaks the two consumers of this port

- biology/gemma: has a conflict with cblas, and is makred broken.

PR:		241363
Exp-run by:	antoine
13 Aug 2019 16:00:39
Original commit files touched by this commit  1.9
Revision:508834
mat search for other commits by this committer
Convert to UCL & cleanup pkg-message (categories a-c)
02 Aug 2018 19:30:57
Original commit files touched by this commit  1.9
Revision:476247
fernape search for other commits by this committer
biology/bcftools: update to 1.9

While here:

* Update LICENSE handling
* Move all commands to bin/

PR:	230169
Submitted by:	ndowens.fbsd@yandex.com
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D16543
23 Jun 2018 08:27:14
Original commit files touched by this commit  1.6_1
Revision:473116
tcberner search for other commits by this committer
Update math/gsl to 2.5

PR:		229067
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  1.6
Revision:452840
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
03 Jul 2017 20:38:12
Original commit files touched by this commit  1.3.1_2
Revision:444988
tcberner search for other commits by this committer
Update math/gsl to 2.4

Exp-Run by:	antoine
PR:		220408
02 May 2017 05:26:40
Original commit files touched by this commit  1.3.1_1
Revision:439928
tcberner search for other commits by this committer
Update math/gsl to 2.3

This release introduces some new features and fixes several bugs:
	http://savannah.gnu.org/forum/forum.php?forum_id=8751

* update to 2.3 and take maintainership
* update math/py-gsl to 2.2.0 for gsl2 support
* update math/rubygem-rb-gsl to 2.1.0.2 for gsl2 support

PR:		218952
Exp-run by:	antoine
Reviewed by:	mat, rakuco
Approved by:	rakuco (mentor)
Differential Revision:	https://reviews.freebsd.org/D10522
26 May 2016 20:28:55
Original commit files touched by this commit  1.3.1
Revision:415914
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  1.3
Revision:415503
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  1.3
Revision:412344
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
25 Dec 2015 01:31:09
Original commit files touched by this commit  1.3
Revision:404398
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)
05 Jun 2015 21:01:14
Original commit files touched by this commit  1.2
Revision:388638
pi search for other commits by this committer
New port: biology/bcftools

BCFtools is a set of utilities that manipulate variant calls in the
Variant Call Format (VCF) and its binary counterpart BCF. All
commands work transparently with both VCFs and BCFs, both
uncompressed and BGZF-compressed.

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

PR:		199747
Submitted by:	cartwright@asu.edu

Number of commits found: 16

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