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Port details
hisat2 Alignment program for mapping next-generation sequencing reads
2.1.0.23 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: 2019-01-11 16:02:24
Last Update: 2019-01-11 16:02:05
SVN Revision: 489981
Also Listed In: perl5 python
License: GPLv3
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).

WWW: https://ccb.jhu.edu/software/hisat2/index.shtml
SVNWeb : Homepage : PortsMon
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (84 items)
  1. /usr/local/share/licenses/hisat2-2.1.0.23/catalog.mk
  2. /usr/local/share/licenses/hisat2-2.1.0.23/LICENSE
  3. /usr/local/share/licenses/hisat2-2.1.0.23/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. libexec/hisat2/compare_HLA_Omixon.py
  14. libexec/hisat2/convert_quals.pl
  15. libexec/hisat2/extract_Omixon_HLA.py
  16. libexec/hisat2/extract_exons.py
  17. libexec/hisat2/extract_splice_sites.py
  18. libexec/hisat2/gen_2b_occ_lookup.pl
  19. libexec/hisat2/gen_occ_lookup.pl
  20. libexec/hisat2/gen_solqual_lookup.pl
  21. libexec/hisat2/hisat2_extract_exons.py
  22. libexec/hisat2/hisat2_extract_snps_haplotypes_UCSC.py
  23. libexec/hisat2/hisat2_extract_snps_haplotypes_VCF.py
  24. libexec/hisat2/hisat2_extract_splice_sites.py
  25. libexec/hisat2/hisat2_simulate_reads.py
  26. libexec/hisat2/hisatgenotype.py
  27. libexec/hisat2/hisatgenotype_HLA_genotyping_PGs.py
  28. libexec/hisat2/hisatgenotype_assembly_graph.py
  29. libexec/hisat2/hisatgenotype_build_genome.py
  30. libexec/hisat2/hisatgenotype_convert_codis.py
  31. libexec/hisat2/hisatgenotype_extract_codis_data.py
  32. libexec/hisat2/hisatgenotype_extract_cyp_data.py
  33. libexec/hisat2/hisatgenotype_extract_reads.py
  34. libexec/hisat2/hisatgenotype_extract_vars.py
  35. libexec/hisat2/hisatgenotype_gene_typing.py
  36. libexec/hisat2/hisatgenotype_hla_cyp.py
  37. libexec/hisat2/hisatgenotype_locus.py
  38. libexec/hisat2/hisatgenotype_locus_samples.py
  39. libexec/hisat2/hisatgenotype_typing_common.py
  40. libexec/hisat2/infer_fraglen.pl
  41. libexec/hisat2/make_a_thaliana_tair.sh
  42. libexec/hisat2/make_b_taurus_UMD3.sh
  43. libexec/hisat2/make_bdgp6.sh
  44. libexec/hisat2/make_bdgp6_tran.sh
  45. libexec/hisat2/make_canFam2.sh
  46. libexec/hisat2/make_ce10.sh
  47. libexec/hisat2/make_dm6.sh
  48. libexec/hisat2/make_e_coli.sh
  49. libexec/hisat2/make_grch37.sh
  50. libexec/hisat2/make_grch37_snp.sh
  51. libexec/hisat2/make_grch37_snp_tran.sh
  52. libexec/hisat2/make_grch37_snp_tran_ercc.sh
  53. libexec/hisat2/make_grch37_tran.sh
  54. libexec/hisat2/make_grch38.sh
  55. libexec/hisat2/make_grch38_snp.sh
  56. libexec/hisat2/make_grch38_snp_tran.sh
  57. libexec/hisat2/make_grch38_snp_tran_ercc.sh
  58. libexec/hisat2/make_grch38_tran.sh
  59. libexec/hisat2/make_grcm38.sh
  60. libexec/hisat2/make_grcm38_snp.sh
  61. libexec/hisat2/make_grcm38_snp_tran.sh
  62. libexec/hisat2/make_grcm38_tran.sh
  63. libexec/hisat2/make_hg19.sh
  64. libexec/hisat2/make_hg38.sh
  65. libexec/hisat2/make_hg38_allsnp.sh
  66. libexec/hisat2/make_hg38_snp.sh
  67. libexec/hisat2/make_hg38_snp_tran.sh
  68. libexec/hisat2/make_mm10.sh
  69. libexec/hisat2/make_mm9.sh
  70. libexec/hisat2/make_r64.sh
  71. libexec/hisat2/make_r64_tran.sh
  72. libexec/hisat2/make_rn4.sh
  73. libexec/hisat2/make_rn6.sh
  74. libexec/hisat2/make_rnor6.sh
  75. libexec/hisat2/make_rnor6_tran.sh
  76. libexec/hisat2/make_sc3.sh
  77. libexec/hisat2/make_wbcel235.sh
  78. libexec/hisat2/make_wbcel235_tran.sh
  79. libexec/hisat2/make_zm3_snp_tran_ercc.sh
  80. libexec/hisat2/run_extract_CP.sh
  81. libexec/hisat2/run_extract_ILMN.sh
  82. libexec/hisat2/run_genotype_build.sh
  83. libexec/hisat2/run_hisat2_build.sh
  84. libexec/hisat2/run_type_CP.sh
  85. Collapse this list.

Dependency line: hisat2>0:biology/hisat2


To install the port: cd /usr/ports/biology/hisat2/ && make install clean
To add the package: pkg install hisat2

PKGNAME: hisat2

There is no flavor information for this port.

ONLY_FOR_ARCHS: amd64

distinfo:

TIMESTAMP = 1547001889
SHA256 (infphilo-hisat2-2.1.0-23-g20f333e_GH0.tar.gz) = 7327fa50f51cd1a0fefe1a379cfeb2f06eefdbbe8f49b04b0d79332080f6be57
SIZE (infphilo-hisat2-2.1.0-23-g20f333e_GH0.tar.gz) = 3972398


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

Build dependencies:
  1. gmake : devel/gmake
  2. python2.7 : lang/python27
  3. perl5>=5.28.r1<5.29 : lang/perl5.28
Runtime dependencies:
  1. python2.7 : lang/python27
  2. perl5>=5.28.r1<5.29 : lang/perl5.28
There are no ports dependent upon this port

Configuration Options
     No options to configure

USES:
gmake perl5 python shebangfix

Master Sites:
  1. https://codeload.github.com/infphilo/hisat2/tar.gz/2.1.0-23-g20f333e?dummy=/

Number of commits found: 1

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
11 Jan 2019 16:02:05
Original commit files touched by this commit  2.1.0.23
Revision:489981
jwb search for other commits by this committer
New port: biology/hisat2: Program for mapping next-generation sequencing reads

Approved by:    jrm (mentor, implicit)

Number of commits found: 1

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