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Port details on branch 2022Q3
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 1.3.1Version 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: 2023-11-06 10:03:47
Commit Hash: 06df180
License: ART10
WWW:
https://bowtie-bio.sourceforge.net/index.shtml
Description:
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.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
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:
TIMESTAMP = 1639406970 SHA256 (BenLangmead-bowtie-v1.3.1_GH0.tar.gz) = 147d9fe9652f7c5f351bfc0eb012e06981986fb43bd6bdfe88a95c02eabc6573 SIZE (BenLangmead-bowtie-v1.3.1_GH0.tar.gz) = 7672741
Packages (timestamps in pop-ups are UTC):
bowtie
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest1.3.11.3.1------
FreeBSD:13:quarterly1.3.11.3.1----1.3.11.3.1
FreeBSD:14:latest1.3.11.3.1-----1.3.1
FreeBSD:14:quarterly1.3.11.3.1----1.3.11.3.1
FreeBSD:15:latest1.3.11.3.1n/a-n/a-1.3.11.3.1
FreeBSD:15:quarterly--n/a-n/a---
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>=5.36<5.37 : lang/perl5.36
There are no ports dependent upon this port
Configuration Options:
===> The following configuration options are available for bowtie-1.3.1: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings
Options name:
biology_bowtie
USES:
compiler:c++11-lib gmake perl5 python:run shebangfix
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.

There are no commits on branch 2022Q3 for this port
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