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test-nginx01 & pg02
Port details
bowtie Ultrafast, memory-efficient short read aligner
1.1.2_5 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: 05 Mar 2016 13:21:35
License: ART10
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
SVNWeb : Homepage : PortsMon
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (92 items)
  1. /usr/local/share/licenses/bowtie-1.1.2_5/catalog.mk
  2. /usr/local/share/licenses/bowtie-1.1.2_5/LICENSE
  3. /usr/local/share/licenses/bowtie-1.1.2_5/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
  93. Collapse this list.

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

PKGNAME: bowtie

ONLY_FOR_ARCHS: amd64

distinfo:

SHA256 (BenLangmead-bowtie-v1.1.2_GH0.tar.gz) = 717145f12d599e9b3672981f5444fbbdb8e02bfde2a80eba577e28baa4125ba7
SIZE (BenLangmead-bowtie-v1.1.2_GH0.tar.gz) = 7831346


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

Build dependencies:
  1. gmake : devel/gmake
  2. gcc6 : lang/gcc6
  3. as : devel/binutils
Runtime dependencies:
  1. python2.7 : lang/python27
  2. gcc6 : lang/gcc6
  3. perl5>=5.24<5.25 : lang/perl5.24
There are no ports dependent upon this port

Configuration Options
     No options to configure

USES:
gmake perl5 python:run shebangfix

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

Number of commits found: 7

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
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: 7

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