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Port details on branch 2022Q3
bowtie2 Ultrafast, memory-efficient short read aligner
2.5.3 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 2.5.2Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2016-03-23 11:22:47
Last Update: 2024-01-18 23:20:08
Commit Hash: 6bb47af
Also Listed In: perl5 python
License: GPLv3+
WWW:
https://github.com/BenLangmead/bowtie2
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 (73 items)
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  1. /usr/local/share/licenses/bowtie2-2.5.3/catalog.mk
  2. /usr/local/share/licenses/bowtie2-2.5.3/LICENSE
  3. /usr/local/share/licenses/bowtie2-2.5.3/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. bin/bowtie2-test
  14. share/bowtie2/scripts/bowtie2-hbb.sh
  15. share/bowtie2/scripts/convert_quals.pl
  16. share/bowtie2/scripts/gen_2b_occ_lookup.pl
  17. share/bowtie2/scripts/gen_occ_lookup.pl
  18. share/bowtie2/scripts/gen_solqual_lookup.pl
  19. share/bowtie2/scripts/infer_fraglen.pl
  20. share/bowtie2/scripts/make_a_thaliana_tair.sh
  21. share/bowtie2/scripts/make_b_taurus_UMD3.sh
  22. share/bowtie2/scripts/make_c_elegans.sh
  23. share/bowtie2/scripts/make_canFam2.sh
  24. share/bowtie2/scripts/make_d_melanogaster.sh
  25. share/bowtie2/scripts/make_e_coli.sh
  26. share/bowtie2/scripts/make_h_sapiens_ncbi36.sh
  27. share/bowtie2/scripts/make_h_sapiens_ncbi37.sh
  28. share/bowtie2/scripts/make_hg18.sh
  29. share/bowtie2/scripts/make_hg19.sh
  30. share/bowtie2/scripts/make_m_musculus_ncbi37.sh
  31. share/bowtie2/scripts/make_mm10.sh
  32. share/bowtie2/scripts/make_mm9.sh
  33. share/bowtie2/scripts/make_rn4.sh
  34. share/bowtie2/scripts/make_s_cerevisiae.sh
  35. share/doc/bowtie2/README
  36. share/doc/bowtie2/images/bowtie_logo.png
  37. share/doc/bowtie2/images/osi-certified.gif
  38. share/doc/bowtie2/images/sflogo.png
  39. share/doc/bowtie2/images/university.small.horizontal.white.png
  40. share/doc/bowtie2/manual.html
  41. share/doc/bowtie2/release.txt
  42. share/doc/bowtie2/style.css
  43. share/doc/bowtie2/website/faq.shtml
  44. share/doc/bowtie2/website/faq.ssi
  45. share/doc/bowtie2/website/foot.ssi
  46. share/doc/bowtie2/website/index.html
  47. share/doc/bowtie2/website/index.shtml
  48. share/doc/bowtie2/website/manual.shtml
  49. share/doc/bowtie2/website/manual.ssi
  50. share/doc/bowtie2/website/news.shtml
  51. share/doc/bowtie2/website/old_news.ssi
  52. share/doc/bowtie2/website/other_tools.shtml
  53. share/doc/bowtie2/website/push.sh
  54. share/doc/bowtie2/website/push_images.sh
  55. share/doc/bowtie2/website/recent_news.ssi
  56. share/doc/bowtie2/website/rhsidebar.ssi
  57. share/doc/bowtie2/website/top.ssi
  58. share/examples/bowtie2/index/lambda_virus.1.bt2
  59. share/examples/bowtie2/index/lambda_virus.2.bt2
  60. share/examples/bowtie2/index/lambda_virus.3.bt2
  61. share/examples/bowtie2/index/lambda_virus.4.bt2
  62. share/examples/bowtie2/index/lambda_virus.rev.1.bt2
  63. share/examples/bowtie2/index/lambda_virus.rev.2.bt2
  64. share/examples/bowtie2/reads/combined_reads.bam
  65. share/examples/bowtie2/reads/conversion_utilities.sh
  66. share/examples/bowtie2/reads/longreads.fq
  67. share/examples/bowtie2/reads/reads_1.fq
  68. share/examples/bowtie2/reads/reads_2.fq
  69. share/examples/bowtie2/reads/simulate.pl
  70. share/examples/bowtie2/reference/lambda_virus.fa
  71. @owner
  72. @group
  73. @mode
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Dependency lines:
  • bowtie2>0:biology/bowtie2
To install the port:
cd /usr/ports/biology/bowtie2/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/bowtie2
  • pkg install bowtie2
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: bowtie2
Flavors: there is no flavor information for this port.
ONLY_FOR_ARCHS: aarch64 amd64 powerpc64 powerpc64le
distinfo:
TIMESTAMP = 1705618664 SHA256 (BenLangmead-bowtie2-v2.5.3_GH0.tar.gz) = 4ac3ece3db011322caab14678b9d80cfc7f75208cdaf0c58b24a6ea0f1a0a60e SIZE (BenLangmead-bowtie2-v2.5.3_GH0.tar.gz) = 10635819

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SHA256 (simd-everywhere-simde-no-tests-f6a0b3b_GH0.tar.gz) = 9874f22afe8a6cd92770aa194df47db3d0963d80ea233a502b0d557f59763eb8 SIZE (simd-everywhere-simde-no-tests-f6a0b3b_GH0.tar.gz) = 397743

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Packages (timestamps in pop-ups are UTC):
bowtie2
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest2.5.32.5.3------
FreeBSD:13:quarterly2.5.22.5.2----2.5.22.5.2
FreeBSD:14:latest2.5.32.5.3-----2.5.1
FreeBSD:14:quarterly2.5.22.5.2----2.5.22.5.2
FreeBSD:15:latest2.5.32.5.3n/a-n/a-2.5.32.5.3
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
  2. python3.9 : lang/python39
Test dependencies:
  1. python3.9 : lang/python39
Runtime dependencies:
  1. bash : shells/bash
  2. python3.9 : lang/python39
  3. perl5>=5.36<5.37 : lang/perl5.36
This port is required by:
for Run
  1. biology/atac-seq
  2. biology/biostar-tools
  3. biology/chip-seq

Deleted ports which required this port:

Expand this list of 1 deleted port
  1. biology/tophat*
  2. Collapse this list of deleted ports.
* - deleted ports are only shown under the This port is required by section. It was harder to do for the Required section. Perhaps later...

Configuration Options:
===> The following configuration options are available for bowtie2-2.5.3: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings
Options name:
biology_bowtie2
USES:
gmake localbase:ldflags perl5 python shebangfix
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
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  1. https://codeload.github.com/BenLangmead/bowtie2/tar.gz/v2.5.3?dummy=/
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There are no commits on branch 2022Q3 for this port