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Port details
bowtie2 Ultrafast, memory-efficient short read aligner
2.4.4 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 2.4.4Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2016-03-23 11:22:47
Last Update: 2021-05-24 16:35:43
Commit Hash: 4521502
Also Listed In: perl5 python
License: GPLv3+
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (73 items)
Collapse this list.
  1. /usr/local/share/licenses/bowtie2-2.4.4/catalog.mk
  2. /usr/local/share/licenses/bowtie2-2.4.4/LICENSE
  3. /usr/local/share/licenses/bowtie2-2.4.4/GPLv3+
  4. bin/bowtie2
  5. bin/bowtie2-align-l
  6. bin/bowtie2-align-s
  7. bin/bowtie2-build
  8. bin/bowtie2-build-l
  9. bin/bowtie2-build-s
  10. bin/bowtie2-inspect
  11. bin/bowtie2-inspect-l
  12. bin/bowtie2-inspect-s
  13. bin/bowtie2-test
  14. share/bowtie2/scripts/bowtie2-hbb.sh
  15. share/bowtie2/scripts/convert_quals.pl
  16. share/bowtie2/scripts/gen_2b_occ_lookup.pl
  17. share/bowtie2/scripts/gen_occ_lookup.pl
  18. share/bowtie2/scripts/gen_solqual_lookup.pl
  19. share/bowtie2/scripts/infer_fraglen.pl
  20. share/bowtie2/scripts/make_a_thaliana_tair.sh
  21. share/bowtie2/scripts/make_b_taurus_UMD3.sh
  22. share/bowtie2/scripts/make_c_elegans.sh
  23. share/bowtie2/scripts/make_canFam2.sh
  24. share/bowtie2/scripts/make_d_melanogaster.sh
  25. share/bowtie2/scripts/make_e_coli.sh
  26. share/bowtie2/scripts/make_h_sapiens_ncbi36.sh
  27. share/bowtie2/scripts/make_h_sapiens_ncbi37.sh
  28. share/bowtie2/scripts/make_hg18.sh
  29. share/bowtie2/scripts/make_hg19.sh
  30. share/bowtie2/scripts/make_m_musculus_ncbi37.sh
  31. share/bowtie2/scripts/make_mm10.sh
  32. share/bowtie2/scripts/make_mm9.sh
  33. share/bowtie2/scripts/make_rn4.sh
  34. share/bowtie2/scripts/make_s_cerevisiae.sh
  35. share/doc/bowtie2/README
  36. share/doc/bowtie2/images/bowtie_logo.png
  37. share/doc/bowtie2/images/osi-certified.gif
  38. share/doc/bowtie2/images/sflogo.png
  39. share/doc/bowtie2/images/university.small.horizontal.white.png
  40. share/doc/bowtie2/manual.html
  41. share/doc/bowtie2/release.txt
  42. share/doc/bowtie2/style.css
  43. share/doc/bowtie2/website/faq.shtml
  44. share/doc/bowtie2/website/faq.ssi
  45. share/doc/bowtie2/website/foot.ssi
  46. share/doc/bowtie2/website/index.html
  47. share/doc/bowtie2/website/index.shtml
  48. share/doc/bowtie2/website/manual.shtml
  49. share/doc/bowtie2/website/manual.ssi
  50. share/doc/bowtie2/website/news.shtml
  51. share/doc/bowtie2/website/old_news.ssi
  52. share/doc/bowtie2/website/other_tools.shtml
  53. share/doc/bowtie2/website/push.sh
  54. share/doc/bowtie2/website/push_images.sh
  55. share/doc/bowtie2/website/recent_news.ssi
  56. share/doc/bowtie2/website/rhsidebar.ssi
  57. share/doc/bowtie2/website/top.ssi
  58. share/examples/bowtie2/index/lambda_virus.1.bt2
  59. share/examples/bowtie2/index/lambda_virus.2.bt2
  60. share/examples/bowtie2/index/lambda_virus.3.bt2
  61. share/examples/bowtie2/index/lambda_virus.4.bt2
  62. share/examples/bowtie2/index/lambda_virus.rev.1.bt2
  63. share/examples/bowtie2/index/lambda_virus.rev.2.bt2
  64. share/examples/bowtie2/reads/combined_reads.bam
  65. share/examples/bowtie2/reads/conversion_utilities.sh
  66. share/examples/bowtie2/reads/longreads.fq
  67. share/examples/bowtie2/reads/reads_1.fq
  68. share/examples/bowtie2/reads/reads_2.fq
  69. share/examples/bowtie2/reads/simulate.pl
  70. share/examples/bowtie2/reference/lambda_virus.fa
  71. @owner
  72. @group
  73. @mode
Collapse this list.
Dependency lines:
  • bowtie2>0:biology/bowtie2
To install the port: cd /usr/ports/biology/bowtie2/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/bowtie2
  • pkg install bowtie2
PKGNAME: bowtie2
Flavors: there is no flavor information for this port.
ONLY_FOR_ARCHS: aarch64 amd64 powerpc64 powerpc64le
distinfo:
Packages (timestamps in pop-ups are UTC):
bowtie2
ABIlatestquarterly
FreeBSD:11:aarch64--
FreeBSD:11:amd642.4.42.4.4
FreeBSD:11:armv6--
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64-2.4.4
FreeBSD:12:amd642.4.42.4.4
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i386--
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64-2.4.4
FreeBSD:13:amd642.4.42.4.4
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i386--
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64-2.4.4
FreeBSD:14:aarch642.4.4-
FreeBSD:14:amd642.4.4-
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i386--
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
 

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. python3.8 : lang/python38
Runtime dependencies:
  1. bash : shells/bash
  2. python3.8 : lang/python38
  3. perl5>=5.32.r0<5.33 : lang/perl5.32
This port is required by:
for Run
  1. biology/biostar-tools

Deleted ports which required this port:

Expand this list of 1 deleted port
  1. biology/tophat*
  2. Collapse this list of deleted ports.
* - deleted ports are only shown under the This port is required by section. It was harder to do for the Required section. Perhaps later...

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/BenLangmead/bowtie2/tar.gz/v2.4.4?dummy=/
Collapse this list.

Number of commits found: 28

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
24 May 2021 16:35:43
 files touched by this commit commit hash:4521502b9bd34932d3547b69cd5aea3c221fad88  2.4.4
jwb search for other commits by this committer
biology/bowtie2: Update to 2.4.4

Fix deadlock issue in multithreaded execution

Reported by:    portscout
17 May 2021 23:40:15
 files touched by this commit commit hash:1effaacbafd70e1bcf3e544d6a7b49bad3ca88ef  2.4.3
jwb search for other commits by this committer
biology/bowtie2: Update to 2.4.3

Drop tbb dependency (upstream switched to C++ threads)
Add support for powerpc64

Reported by:    portscout
Tested by:      pkubaj (powerpc64*)
18 Apr 2021 15:53:14
 files touched by this commit commit hash:48ddc73c5822130dd3f00361ec6998eec0a29e6d  2.4.2_4
jwb search for other commits by this committer
biology/bowtie2: Add support for powerpc64le

PR:             255092
Submitted by:   pkubaj
14 Apr 2021 10:08:05
 files touched by this commit commit hash:9ee84848094757a07a41aefc97967e6ae1a43039  2.4.2_4
martymac search for other commits by this committer
devel/onetbb: Update to 2021.2.0 and bump dependencies

Changelog:
https://software.intel.com/content/www/us/en/develop/articles/intel-oneapi-threading-building-blocks-release-notes.html
07 Apr 2021 08:09:01
 files touched by this commit commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  2.4.2_3
mat search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
06 Apr 2021 14:31:07
 files touched by this commit commit hash:305f148f482daf30dcf728039d03d019f88344eb  2.4.2_3
mat search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
19 Feb 2021 15:14:46
Original commit files touched by this commit Revision:566074  2.4.2_3
martymac search for other commits by this committer
Introduce devel/onetbb and mark devel/tbb as legacy

Intel oneAPI tbb 2021.1 (onetbb) has been released[1][2] and has deprecated
several interfaces over tbb 2020, breaking most dependent ports.

Old tbb 2020 will be kept for a certain time to allow transition but will be
removed in a near future as it CONFLICTS with devel/onetbb. New ports should
now use devel/onetbb instead of devel/tbb.

We tried to move a maximum number of dependent ports to devel/onetbb (or
disable dependency when not possible), but some of them still remain stuck
to devel/tbb. Remaining ones have not been identified as major dependencies
themselves and will be fixed as soon as updates are available from upstream.

PR:		252648, 252688 [3], 252683 [4], 252651 [5], 252690 [3], 252693 [3],
	252695 [3], 252696 [3], 252786 [3], 252649, 252868 [6], 252870 [5],
	252684 [7], 252785 [7]
Approved by:	yuri [3], jwb [4], thierry [5], FreeBSD@Shaneware.biz [6],
	maintainer timeout [7]

[1]
https://software.intel.com/content/www/us/en/develop/articles/intel-oneapi-threading-building-blocks-release-notes.html
[2]
https://software.intel.com/content/www/us/en/develop/articles/tbb-revamp.html
30 Jan 2021 17:43:56
Original commit files touched by this commit Revision:563428  2.4.2_2
jwb search for other commits by this committer
biology/bowtie2: Reverse switch to devel/onetbb

Mistakenly believed onetbb was already committed

PR:             252683
30 Jan 2021 17:39:53
Original commit files touched by this commit Revision:563427  2.4.2_1  Sanity Test Failure
jwb search for other commits by this committer
biology/bowtie2: Switch to devel/onetbb

PR:             252683
Submitted by:   martymac
07 Nov 2020 13:47:41
Original commit files touched by this commit Revision:554390  2.4.2
jwb search for other commits by this committer
biology/bowtie2: Upgrade to 2.4.2

Minor bug fix release

Reported by:    portscout
17 Jul 2020 10:12:26
Original commit files touched by this commit Revision:542423  2.4.1_2
martymac search for other commits by this committer
Update devel/tbb to 2020.3 and bump dependent ports' revisions

Changelog: https://github.com/oneapi-src/oneTBB/blob/v2020.3/CHANGES
01 Apr 2020 14:14:52
Original commit files touched by this commit Revision:530219  2.4.1_1
martymac search for other commits by this committer
Update devel/tbb to 2020.2 and bump dependent port's revisions

Changelog: https://github.com/oneapi-src/oneTBB/blob/tbb_2020/CHANGES
01 Mar 2020 16:01:12
Original commit files touched by this commit Revision:527560  2.4.1
jwb search for other commits by this committer
biology/bowtie2: Upgrade to 2.4.1

Numerous bugfixes and enhancements
Enable experimental support for aarch64

Reported by:    portscout
26 Dec 2019 16:25:22
Original commit files touched by this commit Revision:520935  2.3.5.1_2
martymac search for other commits by this committer
Update devel/tbb to 2020.0 and bump dependent ports' revisions [1]

Also, while here, re-generate patches using the makepatch target

[1] Changelog: https://github.com/intel/tbb/blob/v2020.0/CHANGES
25 Sep 2019 10:03:50
Original commit files touched by this commit Revision:512777  2.3.5.1_1
martymac search for other commits by this committer
Update devel/tbb to 2019.8 and bump dependent ports' revisions

Changelog: https://github.com/intel/tbb/blob/tbb_2019/CHANGES
24 Apr 2019 17:41:28
Original commit files touched by this commit Revision:499873  2.3.5.1
jwb search for other commits by this committer
biology/bowtie2: Clarify CPU-specificity
21 Apr 2019 15:23:26
Original commit files touched by this commit Revision:499544  2.3.5.1
jwb search for other commits by this committer
biology/bowtie2: Upgrade to 2.3.5.1

Disable aarch64.  Upstream support has changed and I lack the resources
to develop new patches.
29 Mar 2019 22:13:11
Original commit files touched by this commit Revision:497212  2.3.5
linimon search for other commits by this committer
Mark as broken on aarch64:

  usage: dirname string [...]

My guess is that some parameter is being passed the empty string.

Approved by:	portmgr (tier-2 blanket)
18 Mar 2019 17:30:25
Original commit files touched by this commit Revision:496155  2.3.5
jwb search for other commits by this committer
biology/bowtie2: Upgrade to 2.3.5

-   Add bowtie2-test script
-   Separate Makefile patches into a static patch for upstream and reinplace
    for ports-specifics
-   Allow aarch64 per upstream Makefile (untested)
11 Oct 2018 14:47:14
Original commit files touched by this commit Revision:481833  2.3.3.1_2
martymac search for other commits by this committer
Update devel/tbb to version 2019.1 and bump dependent ports' revisions

Also, reintegrate HTML documentation that was removed in previous version.
04 Oct 2018 10:03:59
Original commit files touched by this commit Revision:481215  2.3.3.1_1
martymac search for other commits by this committer
Update devel/tbb to version 2019 and bump dependent port's revisions
30 Nov 2017 02:59:16
Original commit files touched by this commit Revision:455161  2.3.3.1
jwb search for other commits by this committer
biology/bowtie2: Upgrade to 2.3.3.1

Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D13300
17 Sep 2017 07:03:14
Original commit files touched by this commit Revision:449986  2.3.0_2
martymac search for other commits by this committer
Update tbb to 2018 and bump dependent ports' revisions
07 Mar 2017 12:44:41
Original commit files touched by this commit Revision:435599  2.3.0_1
martymac search for other commits by this committer
Update devel/tbb to 2017.5

Also bring the following changes:
- Fetch distfiles from Github
- Bump dependent ports' PORTREVISIONs
27 Feb 2017 14:08:30
Original commit files touched by this commit Revision:434940  2.3.0
jbeich search for other commits by this committer
biology/bowtie2: update to 2.3.0

- Unbreak with Clang 4.0

Changes:	https://github.com/BenLangmead/bowtie2/releases/tag/v2.3.0
PR:		216619
Submitted by:	Jason Bacon <bacon4000@gmail.com> (maintainer)
20 Dec 2016 17:01:27
Original commit files touched by this commit Revision:429003  2.2.9
jrm search for other commits by this committer
biology/bowtie2: Update to version 2.2.9

- Update license information.
- Add python to USES (bowtie2-build bowtie2-inspect need python)
- Add DOCS and EXAMPLES options

Approved by:	AMDmi3 (mentor) swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D8182
13 May 2016 20:12:44
Original commit files touched by this commit Revision:415148  2.2.8
pi search for other commits by this committer
biology/bowtie2: 2.2.7 -> 2.2.8

- Various website updates
- Fixed the bowtie2-build issue that made TBB compilation fail

PR:		208943
Submitted by:	Joseph Mingrone <jrm@ftfl.ca>
Approved by:	Jason Bacon <bacon4000@gmail.com> (maintainer)
23 Mar 2016 11:22:39
Original commit files touched by this commit Revision:411698  2.2.7
rakuco search for other commits by this committer
New port: biology/bowtie2.

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short
DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp
reads per hour.

This is Bowtie version 2, which will need to coexists with Bowtie 1 for the
foreseeable future. Both are required by certain genomics pipelines, in some
cases (e.g. Trinity) by the same pipeline.

WWW: https://github.com/BenLangmead/bowtie2

PR:		207908
Submitted by:	Jason Bacon <bacon4000@gmail.com>

Number of commits found: 28