notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)
Ukraine
NOTE: There is a known problem on production with searching pkg-plist - it returns no results. This problem is not present on stage.freshports.org
Port details
bowtie Ultrafast, memory-efficient short read aligner
1.3.1 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: 2016-03-05 13:21:35
Last Update: 2022-09-07 21:58:51
Commit Hash: fb16dfe
License: ART10
Description:
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb
pkg-plist: as obtained via: make generate-plist
Expand this list (98 items)
Collapse this list.
  1. /usr/local/share/licenses/bowtie-1.3.1/catalog.mk
  2. /usr/local/share/licenses/bowtie-1.3.1/LICENSE
  3. /usr/local/share/licenses/bowtie-1.3.1/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/reads/e_coli_1000_interleaved.fq
  33. share/bowtie/scripts/best_verify.pl
  34. share/bowtie/scripts/bowtie-hbb.sh
  35. share/bowtie/scripts/bs_mapability.pl
  36. share/bowtie/scripts/build_test.sh
  37. share/bowtie/scripts/colorize_fasta.pl
  38. share/bowtie/scripts/colorize_fastq.pl
  39. share/bowtie/scripts/convert_quals.pl
  40. share/bowtie/scripts/fastq_to_tabbed.pl
  41. share/bowtie/scripts/gen_2b_occ_lookup.pl
  42. share/bowtie/scripts/gen_dnamasks2colormask.pl
  43. share/bowtie/scripts/gen_occ_lookup.pl
  44. share/bowtie/scripts/gen_solqual_lookup.pl
  45. share/bowtie/scripts/infer_fraglen.pl
  46. share/bowtie/scripts/make_a_thaliana_tair.sh
  47. share/bowtie/scripts/make_b_taurus_UMD3.sh
  48. share/bowtie/scripts/make_c_elegans.sh
  49. share/bowtie/scripts/make_canFam2.sh
  50. share/bowtie/scripts/make_d_melanogaster.sh
  51. share/bowtie/scripts/make_e_coli.sh
  52. share/bowtie/scripts/make_galGal3.sh
  53. share/bowtie/scripts/make_h_sapiens_ncbi36.sh
  54. share/bowtie/scripts/make_h_sapiens_ncbi37.sh
  55. share/bowtie/scripts/make_hg18.sh
  56. share/bowtie/scripts/make_hg19.sh
  57. share/bowtie/scripts/make_m_musculus_ncbi37.sh
  58. share/bowtie/scripts/make_mm8.sh
  59. share/bowtie/scripts/make_mm9.sh
  60. share/bowtie/scripts/make_rn4.sh
  61. share/bowtie/scripts/make_s_cerevisiae.sh
  62. share/bowtie/scripts/mapability.pl
  63. share/bowtie/scripts/pe_verify.pl
  64. share/bowtie/scripts/reconcile_alignments.pl
  65. share/bowtie/scripts/reconcile_alignments_pe.pl
  66. share/bowtie/scripts/run-hbb.sh
  67. share/doc/bowtie/README
  68. share/doc/bowtie/manual.html
  69. share/doc/bowtie/release.txt
  70. share/doc/bowtie/strip_markdown.pl
  71. share/doc/bowtie/style.css
  72. share/doc/bowtie/website/css/style.css
  73. share/doc/bowtie/website/foot.ssi
  74. share/doc/bowtie/website/images/bowtie_logo.png
  75. share/doc/bowtie/website/images/osi-certified.gif
  76. share/doc/bowtie/website/images/sflogo.png
  77. share/doc/bowtie/website/images/university.small.horizontal.white.png
  78. share/doc/bowtie/website/index.html
  79. share/doc/bowtie/website/index.shtml
  80. share/doc/bowtie/website/latest-version.txt
  81. share/doc/bowtie/website/manual.html
  82. share/doc/bowtie/website/manual.shtml
  83. share/doc/bowtie/website/manual.ssi
  84. share/doc/bowtie/website/md5s.shtml
  85. share/doc/bowtie/website/md5s.ssi
  86. share/doc/bowtie/website/news.shtml
  87. share/doc/bowtie/website/old_news.ssi
  88. share/doc/bowtie/website/other_tools.shtml
  89. share/doc/bowtie/website/other_tools.ssi
  90. share/doc/bowtie/website/push.sh
  91. share/doc/bowtie/website/recent_news.ssi
  92. share/doc/bowtie/website/rhsidebar.ssi
  93. share/doc/bowtie/website/top.ssi
  94. share/doc/bowtie/website/tutorial.html
  95. share/doc/bowtie/website/tutorial.shtml
  96. @owner
  97. @group
  98. @mode
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, run one of these commands:
  • pkg install biology/bowtie
  • pkg install bowtie
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: bowtie
Flavors: there is no flavor information for this port.
ONLY_FOR_ARCHS: aarch64 amd64 powerpc64 powerpc64le riscv64
distinfo:

Packages (timestamps in pop-ups are UTC):
bowtie
ABIlatestquarterly
FreeBSD:11:aarch64pkg-falloutpkg-fallout
FreeBSD:11:amd641.1.2_91.1.2_9
FreeBSD:11:armv6pkg-falloutpkg-fallout
FreeBSD:11:i386pkg-falloutpkg-fallout
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips64pkg-falloutpkg-fallout
FreeBSD:12:aarch64pkg-fallout1.3.1
FreeBSD:12:amd641.3.11.3.1
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:aarch641.3.11.3.1
FreeBSD:13:amd641.3.11.3.1
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-falloutpkg-fallout
FreeBSD:13:riscv64pkg-fallout1.3.1
FreeBSD:14:aarch641.3.1pkg-fallout
FreeBSD:14:amd641.3.1pkg-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:powerpc64pkg-falloutpkg-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
Runtime dependencies:
  1. python3.9 : lang/python39
  2. perl5>=5.32.r0<5.33 : lang/perl5.32
There are no ports dependent upon this port

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/bowtie/tar.gz/v1.3.1?dummy=/
Collapse this list.

Number of commits found: 21

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
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)
1.3.1
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)
1.3.1
15 Dec 2021 12:55:57
commit hash:1cbb6054ad0130b8fa50b7a5c32b2f2730bdc977commit hash:1cbb6054ad0130b8fa50b7a5c32b2f2730bdc977commit hash:1cbb6054ad0130b8fa50b7a5c32b2f2730bdc977commit hash:1cbb6054ad0130b8fa50b7a5c32b2f2730bdc977 files touched by this commit
Piotr Kubaj (pkubaj) search for other commits by this committer
biology/bowtie: enable on riscv64
1.3.1
14 Dec 2021 01:43:44
commit hash:eb67c2b94c0b5846d825da791060e0b4c72fc248commit hash:eb67c2b94c0b5846d825da791060e0b4c72fc248commit hash:eb67c2b94c0b5846d825da791060e0b4c72fc248commit hash:eb67c2b94c0b5846d825da791060e0b4c72fc248 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/bowtie: Update to 1.3.1

Also adds support for aarch64 and powerpc64*

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

PR:             260389
Reported by:    pkubaj
1.1.2_9
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
1.1.2_9
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.
1.1.2_9
04 Jul 2020 10:46:08
Revision:541191Original commit files touched by this commit
tobik search for other commits by this committer
biology/bowtie: Unbreak build with GCC 10

In file included from ebwt.h:43,
                 from ebwt_build.cpp:11:
processor_support.h:52:22: error: extended character " is not valid in an
identifier
   52 |         std::cerr << "ERROR: please define __cpuid() for this build.\n";
      |                      ^
processor_support.h:52:72: error: extended character " is not valid in an
identifier
   52 |         std::cerr << "ERROR: please define __cpuid() for this build.\n";
      |                                                                      ^

244494/2020-06-10_18h04m44s/logs/errors/bowtie-1.1.2_9.log" REL="NOFOLLOW">http://package18.nyi.freebsd.org/data/121amd64-default-PR244494/2020-06-10_18h04m44s/logs/errors/bowtie-1.1.2_9.log

PR:		246700
1.1.2_9
26 Jul 2019 20:46:57
Revision:507372Original commit files touched by this commit
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
1.1.2_8
12 Dec 2018 01:35:36
Revision:487272Original commit files touched by this commit
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
1.1.2_7
03 Nov 2018 23:24:29
Revision:483954Original commit files touched by this commit
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)
1.1.2_6
03 Nov 2018 23:16:49
Revision:483953Original commit files touched by this commit
jwb search for other commits by this committer
biology/bowtie: Revert previous commit with missing log message
1.1.2_7
03 Nov 2018 21:10:07
Revision:483910Original commit files touched by this commit
jwb search for other commits by this committer
biology/bowtie: Patch
1.1.2_6
10 Sep 2018 13:14:52
Revision:479406Original commit files touched by this commit
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
1.1.2_6
29 Jul 2018 22:18:46
Revision:475857Original commit files touched by this commit
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
1.1.2_5
10 Mar 2018 17:46:06
Revision:464084Original commit files touched by this commit
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).
1.1.2_4
31 Jan 2018 01:07:08
Revision:460452Original commit files touched by this commit
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
1.1.2_4
10 Sep 2017 20:55:39
Revision:449591Original commit files touched by this commit
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
1.1.2_3
22 Apr 2017 09:25:44
Revision:439143Original commit files touched by this commit
miwi search for other commits by this committer
- Fix shebangs
1.1.2_2
01 Apr 2017 15:23:32
Revision:437439Original commit files touched by this commit
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
1.1.2_1
20 Nov 2016 09:38:09
Revision:426566Original commit files touched by this commit
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.
1.1.2
05 Mar 2016 13:21:26
Revision:410180Original commit files touched by this commit
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: 21