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Port details
bowtie2 Ultrafast, memory-efficient short read aligner
2.3.3.1_2 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
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 23 Mar 2016 11:22:47
License: GPLv3+
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.

WWW: https://github.com/BenLangmead/bowtie2
SVNWeb : Homepage : PortsMon
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (66 items)
  1. /usr/local/share/licenses/bowtie2-2.3.3.1_2/catalog.mk
  2. /usr/local/share/licenses/bowtie2-2.3.3.1_2/LICENSE
  3. /usr/local/share/licenses/bowtie2-2.3.3.1_2/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. share/bowtie2/scripts/convert_quals.pl
  14. share/bowtie2/scripts/gen_2b_occ_lookup.pl
  15. share/bowtie2/scripts/gen_occ_lookup.pl
  16. share/bowtie2/scripts/gen_solqual_lookup.pl
  17. share/bowtie2/scripts/infer_fraglen.pl
  18. share/bowtie2/scripts/make_a_thaliana_tair.sh
  19. share/bowtie2/scripts/make_b_taurus_UMD3.sh
  20. share/bowtie2/scripts/make_c_elegans.sh
  21. share/bowtie2/scripts/make_canFam2.sh
  22. share/bowtie2/scripts/make_d_melanogaster.sh
  23. share/bowtie2/scripts/make_e_coli.sh
  24. share/bowtie2/scripts/make_h_sapiens_ncbi36.sh
  25. share/bowtie2/scripts/make_h_sapiens_ncbi37.sh
  26. share/bowtie2/scripts/make_hg18.sh
  27. share/bowtie2/scripts/make_hg19.sh
  28. share/bowtie2/scripts/make_m_musculus_ncbi37.sh
  29. share/bowtie2/scripts/make_mm10.sh
  30. share/bowtie2/scripts/make_mm9.sh
  31. share/bowtie2/scripts/make_rn4.sh
  32. share/bowtie2/scripts/make_s_cerevisiae.sh
  33. share/doc/bowtie2/README
  34. share/doc/bowtie2/images/bowtie_logo.png
  35. share/doc/bowtie2/images/osi-certified.gif
  36. share/doc/bowtie2/images/sflogo.png
  37. share/doc/bowtie2/images/university.small.horizontal.white.png
  38. share/doc/bowtie2/manual.html
  39. share/doc/bowtie2/release.txt
  40. share/doc/bowtie2/style.css
  41. share/doc/bowtie2/website/faq.shtml
  42. share/doc/bowtie2/website/faq.ssi
  43. share/doc/bowtie2/website/foot.ssi
  44. share/doc/bowtie2/website/index.html
  45. share/doc/bowtie2/website/index.shtml
  46. share/doc/bowtie2/website/manual.shtml
  47. share/doc/bowtie2/website/manual.ssi
  48. share/doc/bowtie2/website/news.shtml
  49. share/doc/bowtie2/website/old_news.ssi
  50. share/doc/bowtie2/website/other_tools.shtml
  51. share/doc/bowtie2/website/push.sh
  52. share/doc/bowtie2/website/push_images.sh
  53. share/doc/bowtie2/website/recent_news.ssi
  54. share/doc/bowtie2/website/rhsidebar.ssi
  55. share/doc/bowtie2/website/top.ssi
  56. share/examples/bowtie2/index/lambda_virus.1.bt2
  57. share/examples/bowtie2/index/lambda_virus.2.bt2
  58. share/examples/bowtie2/index/lambda_virus.3.bt2
  59. share/examples/bowtie2/index/lambda_virus.4.bt2
  60. share/examples/bowtie2/index/lambda_virus.rev.1.bt2
  61. share/examples/bowtie2/index/lambda_virus.rev.2.bt2
  62. share/examples/bowtie2/reads/longreads.fq
  63. share/examples/bowtie2/reads/reads_1.fq
  64. share/examples/bowtie2/reads/reads_2.fq
  65. share/examples/bowtie2/reads/simulate.pl
  66. share/examples/bowtie2/reference/lambda_virus.fa
  67. Collapse this list.

To install the port: cd /usr/ports/biology/bowtie2/ && make install clean
To add the package: pkg install bowtie2

PKGNAME: bowtie2

ONLY_FOR_ARCHS: amd64

distinfo:

TIMESTAMP = 1511991430
SHA256 (BenLangmead-bowtie2-v2.3.3.1_GH0.tar.gz) = 8b9c0b9c595ebcddcac5feaf6acb44b2294d6deb91de107596ecad242a1a58e9
SIZE (BenLangmead-bowtie2-v2.3.3.1_GH0.tar.gz) = 5796279


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. gmake : devel/gmake
  2. python2.7 : lang/python27
Runtime dependencies:
  1. python2.7 : lang/python27
  2. perl5>=5.26<5.27 : lang/perl5.26
Library dependencies:
  1. libtbb.so : devel/tbb
There are no ports dependent upon this port

Configuration Options
===> The following configuration options are available for bowtie2-2.3.3.1_2:
     DOCS=on: Build and/or install documentation
     EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings

USES:
gmake perl5 python shebangfix

Master Sites:
  1. https://codeload.github.com/BenLangmead/bowtie2/tar.gz/v2.3.3.1?dummy=/

Number of commits found: 9

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
11 Oct 2018 14:47:14
Original commit files touched by this commit  2.3.3.1_2
Revision:481833
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  2.3.3.1_1
Revision:481215
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  2.3.3.1
Revision:455161
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  2.3.0_2
Revision:449986
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  2.3.0_1
Revision:435599
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  2.3.0
Revision:434940
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  2.2.9
Revision:429003
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  2.2.8
Revision:415148
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  2.2.7
Revision:411698
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: 9

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