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Port details
bowtie Ultrafast, memory-efficient short read aligner
1.1.2_9 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 1.1.2Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2016-03-05 13:21:35
Last Update: 2019-07-26 21:46:57
SVN Revision: 507372
License: ART10
Description:
SVNWeb : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (92 items)
  1. /usr/local/share/licenses/bowtie-1.1.2_9/catalog.mk
  2. /usr/local/share/licenses/bowtie-1.1.2_9/LICENSE
  3. /usr/local/share/licenses/bowtie-1.1.2_9/ART10
  4. bin/bowtie
  5. bin/bowtie-align-l
  6. bin/bowtie-align-s
  7. bin/bowtie-build
  8. bin/bowtie-build-l
  9. bin/bowtie-build-s
  10. bin/bowtie-inspect
  11. bin/bowtie-inspect-l
  12. bin/bowtie-inspect-s
  13. share/bowtie/genomes/.cvsignore
  14. share/bowtie/genomes/NC_008253.fna
  15. share/bowtie/indexes/e_coli.1.ebwt
  16. share/bowtie/indexes/e_coli.2.ebwt
  17. share/bowtie/indexes/e_coli.3.ebwt
  18. share/bowtie/indexes/e_coli.4.ebwt
  19. share/bowtie/indexes/e_coli.README
  20. share/bowtie/indexes/e_coli.rev.1.ebwt
  21. share/bowtie/indexes/e_coli.rev.2.ebwt
  22. share/bowtie/reads/e_coli_1000.fa
  23. share/bowtie/reads/e_coli_1000.fq
  24. share/bowtie/reads/e_coli_1000.raw
  25. share/bowtie/reads/e_coli_10000snp.csfasta
  26. share/bowtie/reads/e_coli_10000snp.fa
  27. share/bowtie/reads/e_coli_10000snp.fq
  28. share/bowtie/reads/e_coli_1000_1.fa
  29. share/bowtie/reads/e_coli_1000_1.fq
  30. share/bowtie/reads/e_coli_1000_2.fa
  31. share/bowtie/reads/e_coli_1000_2.fq
  32. share/bowtie/scripts/best_verify.pl
  33. share/bowtie/scripts/bs_mapability.pl
  34. share/bowtie/scripts/build_test.sh
  35. share/bowtie/scripts/colorize_fasta.pl
  36. share/bowtie/scripts/colorize_fastq.pl
  37. share/bowtie/scripts/convert_quals.pl
  38. share/bowtie/scripts/fastq_to_tabbed.pl
  39. share/bowtie/scripts/gen_2b_occ_lookup.pl
  40. share/bowtie/scripts/gen_dnamasks2colormask.pl
  41. share/bowtie/scripts/gen_occ_lookup.pl
  42. share/bowtie/scripts/gen_solqual_lookup.pl
  43. share/bowtie/scripts/infer_fraglen.pl
  44. share/bowtie/scripts/make_a_thaliana_tair.sh
  45. share/bowtie/scripts/make_b_taurus_UMD3.sh
  46. share/bowtie/scripts/make_c_elegans.sh
  47. share/bowtie/scripts/make_canFam2.sh
  48. share/bowtie/scripts/make_d_melanogaster.sh
  49. share/bowtie/scripts/make_e_coli.sh
  50. share/bowtie/scripts/make_galGal3.sh
  51. share/bowtie/scripts/make_h_sapiens_ncbi36.sh
  52. share/bowtie/scripts/make_h_sapiens_ncbi37.sh
  53. share/bowtie/scripts/make_hg18.sh
  54. share/bowtie/scripts/make_hg19.sh
  55. share/bowtie/scripts/make_m_musculus_ncbi37.sh
  56. share/bowtie/scripts/make_mm8.sh
  57. share/bowtie/scripts/make_mm9.sh
  58. share/bowtie/scripts/make_rn4.sh
  59. share/bowtie/scripts/make_s_cerevisiae.sh
  60. share/bowtie/scripts/mapability.pl
  61. share/bowtie/scripts/pe_verify.pl
  62. share/bowtie/scripts/reconcile_alignments.pl
  63. share/bowtie/scripts/reconcile_alignments_pe.pl
  64. share/doc/bowtie/README
  65. share/doc/bowtie/manual.html
  66. share/doc/bowtie/release.txt
  67. share/doc/bowtie/strip_markdown.pl
  68. share/doc/bowtie/style.css
  69. share/doc/bowtie/website/css/style.css
  70. share/doc/bowtie/website/foot.ssi
  71. share/doc/bowtie/website/images/bowtie_logo.png
  72. share/doc/bowtie/website/images/osi-certified.gif
  73. share/doc/bowtie/website/images/sflogo.png
  74. share/doc/bowtie/website/images/university.small.horizontal.white.png
  75. share/doc/bowtie/website/index.html
  76. share/doc/bowtie/website/index.shtml
  77. share/doc/bowtie/website/latest-version.txt
  78. share/doc/bowtie/website/manual.html
  79. share/doc/bowtie/website/manual.shtml
  80. share/doc/bowtie/website/manual.ssi
  81. share/doc/bowtie/website/md5s.shtml
  82. share/doc/bowtie/website/md5s.ssi
  83. share/doc/bowtie/website/news.shtml
  84. share/doc/bowtie/website/old_news.ssi
  85. share/doc/bowtie/website/other_tools.shtml
  86. share/doc/bowtie/website/other_tools.ssi
  87. share/doc/bowtie/website/push_langmead.sh
  88. share/doc/bowtie/website/recent_news.ssi
  89. share/doc/bowtie/website/rhsidebar.ssi
  90. share/doc/bowtie/website/top.ssi
  91. share/doc/bowtie/website/tutorial.html
  92. share/doc/bowtie/website/tutorial.shtml
Collapse this list.
Dependency lines:
  • bowtie>0:biology/bowtie
To install the port: cd /usr/ports/biology/bowtie/ && make install clean
To add the package: pkg install bowtie
PKGNAME: bowtie
Flavors: there is no flavor information for this port.
ONLY_FOR_ARCHS: amd64
distinfo:

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake : devel/gmake
  2. gcc9 : lang/gcc9
  3. as : devel/binutils
Runtime dependencies:
  1. python3.6 : lang/python36
  2. gcc9 : lang/gcc9
  3. perl5>=5.28.r1<5.29 : lang/perl5.28
There are no ports dependent upon this port

Configuration Options

USES:

Master Sites:
  1. https://codeload.github.com/BenLangmead/bowtie/tar.gz/v1.1.2?dummy=/

Number of commits found: 14

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
26 Jul 2019 20:46:57
Original commit files touched by this commit  1.1.2_9
Revision:507372
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330
12 Dec 2018 01:35:36
Original commit files touched by this commit  1.1.2_8
Revision:487272
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590
03 Nov 2018 23:24:29
Original commit files touched by this commit  1.1.2_7
Revision:483954
jwb search for other commits by this committer
biology/bowtie: Patch for gcc8 and clean up

PR:             232929
Reported by:    gerald
Approved by:    jrm (mentor, implicit)
03 Nov 2018 23:16:49
Original commit files touched by this commit  1.1.2_6
Revision:483953
jwb search for other commits by this committer
biology/bowtie: Revert previous commit with missing log message
03 Nov 2018 21:10:07
Original commit files touched by this commit  1.1.2_7
Revision:483910
jwb search for other commits by this committer
biology/bowtie: Patch
10 Sep 2018 13:14:52
Original commit files touched by this commit  1.1.2_6
Revision:479406
mat search for other commits by this committer
Add DOCS options to ports that should have one.

Also various fixes related to said option.

PR:		230864
Submitted by:	mat
exp-runs by:	antoine
29 Jul 2018 22:18:46
Original commit files touched by this commit  1.1.2_6
Revision:475857
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
in the ports tree (via Mk/bsd.default-versions.mk and lang/gcc) which
has now moved from GCC 6 to GCC 7 by default.

This includes ports
 - featuring USE_GCC=yes or USE_GCC=any,
 - featuring USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and those
 - with USES=compiler specifying one of openmp, nestedfct, c11, c++0x,
   c++11-lib, c++11-lang, c++14-lang, c++17-lang, or gcc-c++11-lib.

PR:		222542
10 Mar 2018 17:46:06
Original commit files touched by this commit  1.1.2_5
Revision:464084
gerald search for other commits by this committer
Bump PORTREVISIONs of all users of math/mpc that we just updated to
version 1.1.0 (via revision 464079).
31 Jan 2018 01:07:08
Original commit files touched by this commit  1.1.2_4
Revision:460452
jwb search for other commits by this committer
Multiple ports:
Change maintainer email bacon4000@gmail.com to jwb@FreeBSD.org
Remove Created by comments for same user

Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D14128
10 Sep 2017 20:55:39
Original commit files touched by this commit  1.1.2_4
Revision:449591
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
(via Mk/bsd.default-versions.mk and lang/gcc) which has moved from
GCC 5.4 to GCC 6.4 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++11-lang,
   c++14-lang, c++0x, c11, or gcc-c++11-lib.

PR:		219275
22 Apr 2017 09:25:44
Original commit files touched by this commit  1.1.2_3
Revision:439143
miwi search for other commits by this committer
- Fix shebangs
01 Apr 2017 15:23:32
Original commit files touched by this commit  1.1.2_2
Revision:437439
gerald search for other commits by this committer
Bump PORTREVISIONs for ports depending on the canonical version of GCC and
lang/gcc which have moved from GCC 4.9.4 to GCC 5.4 (at least under some
circumstances such as versions of FreeBSD or platforms).

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using using Mk/bsd.octave.mk which in turn has USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++14-lang,
   c++11-lang, c++0x, c11, or gcc-c++11-lib.

PR:		216707
20 Nov 2016 09:38:09
Original commit files touched by this commit  1.1.2_1
Revision:426566
gerald search for other commits by this committer
Bump PORTREVISIONS for ports depending on the canonical version of GCC and
lang/gcc which have moved from GCC 4.8.5 to GCC 4.9.4 (at least under some
circumstances such as versions of FreeBSD or platforms).

In particular that is ports with USE_GCC=yes, USE_GCC=any, or one of
gcc-c++11-lib, openmp, nestedfct, c++11-lib as well as c++14-lang,
c++11-lang, c++0x, c11 requested via USES=compiler.
05 Mar 2016 13:21:26
Original commit files touched by this commit  1.1.2
Revision:410180
rakuco search for other commits by this committer
New port: biology/bowtie.

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: http://bowtie-bio.sourceforge.net/index.shtml

PR:		206939
Submitted by:	Jason Bacon <bacon4000@gmail.com>

Number of commits found: 14

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