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We just rebooted with several updates: * new HMTLify code * no port maintainer is now highly visible (e.g. https://freshports.org/security/sssd/) * fixed search logic error when using plain/ text details at https://github.com/FreshPorts/freshports/releases/tag/2.2.34
Port details
bowtie2 Ultrafast, memory-efficient short read aligner
2.5.1 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 Version 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: 2023-01-21 22:30:48
Commit Hash: 65ce3f1
Also Listed In: perl5 python
License: GPLv3+
Description:
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb
pkg-plist: as obtained via: make generate-plist
Expand this list (73 items)
Collapse this list.
  1. /usr/local/share/licenses/bowtie2-2.5.1/catalog.mk
  2. /usr/local/share/licenses/bowtie2-2.5.1/LICENSE
  3. /usr/local/share/licenses/bowtie2-2.5.1/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
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
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:aarch64pkg-falloutpkg-fallout
FreeBSD:11:amd642.4.42.4.4
FreeBSD:11:armv6pkg-falloutpkg-fallout
FreeBSD:11:i386pkg-falloutpkg-fallout
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips64pkg-falloutpkg-fallout
FreeBSD:12:aarch64pkg-fallout2.5.0
FreeBSD:12:amd642.5.12.5.0
FreeBSD:12:armv6pkg-falloutpkg-fallout
FreeBSD:12:armv7pkg-falloutpkg-fallout
FreeBSD:12:i386pkg-falloutpkg-fallout
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips64pkg-falloutpkg-fallout
FreeBSD:12:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:aarch642.5.12.5.0
FreeBSD:13:amd642.5.12.5.0
FreeBSD:13:armv6pkg-falloutpkg-fallout
FreeBSD:13:armv7pkg-falloutpkg-fallout
FreeBSD:13:i386pkg-falloutpkg-fallout
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips64pkg-falloutpkg-fallout
FreeBSD:13:powerpc64pkg-fallout2.5.0
FreeBSD:13:riscv64pkg-falloutpkg-fallout
FreeBSD:14:aarch642.5.0pkg-fallout
FreeBSD:14:amd642.5.1pkg-fallout
FreeBSD:14:armv6pkg-falloutpkg-fallout
FreeBSD:14:armv7pkg-falloutpkg-fallout
FreeBSD:14:i386pkg-falloutpkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips64pkg-falloutpkg-fallout
FreeBSD:14:powerpc642.5.0pkg-fallout
FreeBSD:14:riscv64pkg-falloutpkg-fallout
 

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. python3.9 : lang/python39
Test dependencies:
  1. python3.9 : lang/python39
Runtime dependencies:
  1. bash : shells/bash
  2. python3.9 : lang/python39
  3. perl5>=5.32.r0<5.33 : lang/perl5.32
This port is required by:
for Run
  1. biology/atac-seq
  2. 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/v2.5.1?dummy=/
Collapse this list.

Number of commits found: 35

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
2.5.1
21 Jan 2023 22:30:48
commit hash:65ce3f1684bc6a0457bfc55feb059baf76bbee2acommit hash:65ce3f1684bc6a0457bfc55feb059baf76bbee2acommit hash:65ce3f1684bc6a0457bfc55feb059baf76bbee2acommit hash:65ce3f1684bc6a0457bfc55feb059baf76bbee2a files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/bowtie2: Update to 2.5.1

A few minor fixes and enhancements

Changes:    https://github.com/BenLangmead/bowtie2/tags

Reported by:    portscout
2.5.0
09 Nov 2022 22:50:41
commit hash:12c49822cb56ffc9952960db268c3a556a0ad087commit hash:12c49822cb56ffc9952960db268c3a556a0ad087commit hash:12c49822cb56ffc9952960db268c3a556a0ad087commit hash:12c49822cb56ffc9952960db268c3a556a0ad087 files touched by this commit
Piotr Kubaj (pkubaj) search for other commits by this committer
biology/bowtie2: fix build on powerpc64*
2.5.0
04 Nov 2022 23:49:02
commit hash:f2f8bd75c4acf8a9c1fb5d51a0f381e25a9006facommit hash:f2f8bd75c4acf8a9c1fb5d51a0f381e25a9006facommit hash:f2f8bd75c4acf8a9c1fb5d51a0f381e25a9006facommit hash:f2f8bd75c4acf8a9c1fb5d51a0f381e25a9006fa files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/bowtie2: Update to 2.5.0

Performance improvements and minor improvements
Changes:    https://github.com/BenLangmead/bowtie2/tags

Reported by:    portscout
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)
2.4.5
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)
2.4.5
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)
2.4.5
21 Jan 2022 14:33:54
commit hash:bfdda4387466c93127ca47424f61e03c94aae8bbcommit hash:bfdda4387466c93127ca47424f61e03c94aae8bbcommit hash:bfdda4387466c93127ca47424f61e03c94aae8bbcommit hash:bfdda4387466c93127ca47424f61e03c94aae8bb files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/bowtie2: Update to 2.4.5

A few bug fixes

Changes:        https://github.com/BenLangmead/bowtie2/tags
Reported by:    portscout
2.4.4
24 May 2021 16:35:43
commit hash:4521502b9bd34932d3547b69cd5aea3c221fad88commit hash:4521502b9bd34932d3547b69cd5aea3c221fad88commit hash:4521502b9bd34932d3547b69cd5aea3c221fad88commit hash:4521502b9bd34932d3547b69cd5aea3c221fad88 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/bowtie2: Update to 2.4.4

Fix deadlock issue in multithreaded execution

Reported by:    portscout
2.4.3
17 May 2021 23:40:15
commit hash:1effaacbafd70e1bcf3e544d6a7b49bad3ca88efcommit hash:1effaacbafd70e1bcf3e544d6a7b49bad3ca88efcommit hash:1effaacbafd70e1bcf3e544d6a7b49bad3ca88efcommit hash:1effaacbafd70e1bcf3e544d6a7b49bad3ca88ef files touched by this commit
Jason W. Bacon (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*)
2.4.2_4
18 Apr 2021 15:53:14
commit hash:48ddc73c5822130dd3f00361ec6998eec0a29e6dcommit hash:48ddc73c5822130dd3f00361ec6998eec0a29e6dcommit hash:48ddc73c5822130dd3f00361ec6998eec0a29e6dcommit hash:48ddc73c5822130dd3f00361ec6998eec0a29e6d files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/bowtie2: Add support for powerpc64le

PR:             255092
Submitted by:   pkubaj
2.4.2_4
14 Apr 2021 10:08:05
commit hash:9ee84848094757a07a41aefc97967e6ae1a43039commit hash:9ee84848094757a07a41aefc97967e6ae1a43039commit hash:9ee84848094757a07a41aefc97967e6ae1a43039commit hash:9ee84848094757a07a41aefc97967e6ae1a43039 files touched by this commit
Ganael LAPLANCHE (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
2.4.2_3
07 Apr 2021 08:09:01
commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
2.4.2_3
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.
2.4.2_3
19 Feb 2021 15:14:46
Revision:566074Original commit files touched by this commit
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
2.4.2_2
30 Jan 2021 17:43:56
Revision:563428Original commit files touched by this commit
jwb search for other commits by this committer
biology/bowtie2: Reverse switch to devel/onetbb

Mistakenly believed onetbb was already committed

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

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

Minor bug fix release

Reported by:    portscout
2.4.1_2
17 Jul 2020 10:12:26
Revision:542423Original commit files touched by this commit
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
2.4.1_1
01 Apr 2020 14:14:52
Revision:530219Original commit files touched by this commit
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
2.4.1
01 Mar 2020 16:01:12
Revision:527560Original commit files touched by this commit
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
2.3.5.1_2
26 Dec 2019 16:25:22
Revision:520935Original commit files touched by this commit
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
2.3.5.1_1
25 Sep 2019 10:03:50
Revision:512777Original commit files touched by this commit
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
2.3.5.1
24 Apr 2019 17:41:28
Revision:499873Original commit files touched by this commit
jwb search for other commits by this committer
biology/bowtie2: Clarify CPU-specificity
2.3.5.1
21 Apr 2019 15:23:26
Revision:499544Original commit files touched by this commit
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.
2.3.5
29 Mar 2019 22:13:11
Revision:497212Original commit files touched by this commit
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)
2.3.5
18 Mar 2019 17:30:25
Revision:496155Original commit files touched by this commit
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)
2.3.3.1_2
11 Oct 2018 14:47:14
Revision:481833Original commit files touched by this commit
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.
2.3.3.1_1
04 Oct 2018 10:03:59
Revision:481215Original commit files touched by this commit
martymac search for other commits by this committer
Update devel/tbb to version 2019 and bump dependent port's revisions
2.3.3.1
30 Nov 2017 02:59:16
Revision:455161Original commit files touched by this commit
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
2.3.0_2
17 Sep 2017 07:03:14
Revision:449986Original commit files touched by this commit
martymac search for other commits by this committer
Update tbb to 2018 and bump dependent ports' revisions
2.3.0_1
07 Mar 2017 12:44:41
Revision:435599Original commit files touched by this commit
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
2.3.0
27 Feb 2017 14:08:30
Revision:434940Original commit files touched by this commit
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)
2.2.9
20 Dec 2016 17:01:27
Revision:429003Original commit files touched by this commit
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
2.2.8
13 May 2016 20:12:44
Revision:415148Original commit files touched by this commit
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)
2.2.7
23 Mar 2016 11:22:39
Revision:411698Original commit files touched by this commit
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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: 35