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Port details on branch 2022Q2
hisat2 Alignment program for mapping next-generation sequencing reads
2.2.1_2 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 2.2.1_2Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-01-11 16:02:24
Last Update: 2022-09-07 21:58:51
Commit Hash: fb16dfe
Also Listed In: perl5 python
License: GPLv3
WWW:
https://ccb.jhu.edu/software/hisat2/index.shtml
Description:
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).
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 (72 items)
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  1. /usr/local/share/licenses/hisat2-2.2.1_2/catalog.mk
  2. /usr/local/share/licenses/hisat2-2.2.1_2/LICENSE
  3. /usr/local/share/licenses/hisat2-2.2.1_2/GPLv3
  4. bin/hisat2
  5. bin/hisat2-align-l
  6. bin/hisat2-align-s
  7. bin/hisat2-build
  8. bin/hisat2-build-l
  9. bin/hisat2-build-s
  10. bin/hisat2-inspect
  11. bin/hisat2-inspect-l
  12. bin/hisat2-inspect-s
  13. bin/hisat2-repeat
  14. libexec/hisat2/convert_quals.pl
  15. libexec/hisat2/extract_exons.py
  16. libexec/hisat2/extract_splice_sites.py
  17. libexec/hisat2/gen_2b_occ_lookup.pl
  18. libexec/hisat2/gen_occ_lookup.pl
  19. libexec/hisat2/gen_solqual_lookup.pl
  20. libexec/hisat2/hisat2_extract_exons.py
  21. libexec/hisat2/hisat2_extract_snps_haplotypes_UCSC.py
  22. libexec/hisat2/hisat2_extract_snps_haplotypes_VCF.py
  23. libexec/hisat2/hisat2_extract_splice_sites.py
  24. libexec/hisat2/hisat2_read_statistics.py
  25. libexec/hisat2/hisat2_simulate_reads.py
  26. libexec/hisat2/infer_fraglen.pl
  27. libexec/hisat2/make_a_thaliana_tair.sh
  28. libexec/hisat2/make_b_taurus_UMD3.sh
  29. libexec/hisat2/make_bdgp6.sh
  30. libexec/hisat2/make_bdgp6_tran.sh
  31. libexec/hisat2/make_canFam2.sh
  32. libexec/hisat2/make_ce10.sh
  33. libexec/hisat2/make_dm6.sh
  34. libexec/hisat2/make_e_coli.sh
  35. libexec/hisat2/make_grch37.sh
  36. libexec/hisat2/make_grch37_snp.sh
  37. libexec/hisat2/make_grch37_snp_tran.sh
  38. libexec/hisat2/make_grch37_snp_tran_ercc.sh
  39. libexec/hisat2/make_grch37_tran.sh
  40. libexec/hisat2/make_grch38.sh
  41. libexec/hisat2/make_grch38_rep.sh
  42. libexec/hisat2/make_grch38_snp.sh
  43. libexec/hisat2/make_grch38_snp_rep.sh
  44. libexec/hisat2/make_grch38_snp_tran.sh
  45. libexec/hisat2/make_grch38_snp_tran_ercc.sh
  46. libexec/hisat2/make_grch38_tran.sh
  47. libexec/hisat2/make_grcm38.sh
  48. libexec/hisat2/make_grcm38_snp.sh
  49. libexec/hisat2/make_grcm38_snp_tran.sh
  50. libexec/hisat2/make_grcm38_tran.sh
  51. libexec/hisat2/make_hg19.sh
  52. libexec/hisat2/make_hg38.sh
  53. libexec/hisat2/make_hg38_allsnp.sh
  54. libexec/hisat2/make_hg38_snp.sh
  55. libexec/hisat2/make_hg38_snp_tran.sh
  56. libexec/hisat2/make_mm10.sh
  57. libexec/hisat2/make_mm9.sh
  58. libexec/hisat2/make_r64.sh
  59. libexec/hisat2/make_r64_tran.sh
  60. libexec/hisat2/make_rn4.sh
  61. libexec/hisat2/make_rn6.sh
  62. libexec/hisat2/make_rnor6.sh
  63. libexec/hisat2/make_rnor6_tran.sh
  64. libexec/hisat2/make_sc3.sh
  65. libexec/hisat2/make_wbcel235.sh
  66. libexec/hisat2/make_wbcel235_tran.sh
  67. libexec/hisat2/make_zm3_snp_tran_ercc.sh
  68. libexec/hisat2/sa.py
  69. libexec/hisat2/validate_repeat.py
  70. @owner
  71. @group
  72. @mode
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Dependency lines:
  • hisat2>0:biology/hisat2
To install the port:
cd /usr/ports/biology/hisat2/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/hisat2
  • pkg install hisat2
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: hisat2
Flavors: there is no flavor information for this port.
ONLY_FOR_ARCHS: aarch64 amd64 powerpc64 powerpc64le riscv64
distinfo:
TIMESTAMP = 1637941870 SHA256 (DaehwanKimLab-hisat2-v2.2.1_GH0.tar.gz) = f3f4f867d0a6b1f880d64efc19deaa5788c62050e0a4d614ce98b3492f702599 SIZE (DaehwanKimLab-hisat2-v2.2.1_GH0.tar.gz) = 6761242

Packages (timestamps in pop-ups are UTC):
hisat2
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest2.2.1_22.2.1_2------
FreeBSD:13:quarterly2.2.1_22.2.1_2----2.2.1_22.2.1_2
FreeBSD:14:latest2.2.1_22.2.1_2-----2.2.1_2
FreeBSD:14:quarterly2.2.1_22.2.1_2----2.2.1_22.2.1_2
FreeBSD:15:latest2.2.1_22.2.1_2n/a-n/a-2.2.1_22.2.1_2
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. simde>0 : devel/simde
  2. gmake>=4.3 : devel/gmake
  3. python3.9 : lang/python39
  4. perl5>=5.32.r0<5.33 : lang/perl5.32
Runtime dependencies:
  1. python3.9 : lang/python39
  2. perl5>=5.32.r0<5.33 : lang/perl5.32
This port is required by:
for Run
  1. biology/biostar-tools
  2. biology/rna-seq

Configuration Options:
No options to configure
Options name:
biology_hisat2
USES:
gmake localbase perl5 python 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/DaehwanKimLab/hisat2/tar.gz/v2.2.1?dummy=/
Collapse this list.

There are no commits on branch 2022Q2 for this port