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Port details on branch 2022Q2
hhsuite Remote protein homology detection suite
3.3.0_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 3.3.0_3Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-05-19 06:52:54
Last Update: 2024-02-18 09:29:31
Commit Hash: 9eba616
Also Listed In: science
License: GPLv3
WWW:
https://github.com/soedinglab/hh-suite
Description:
SIMD-vectorized implementation of the Viterbi algorithm for profile HMM alignment and introduced various other speed-ups. This accelerated HHsearch by a factor 4 and HHblits by a factor 2 over the previous version 2.0.16. HHblits3 is ~10x faster than PSI-BLAST and ~20x faster than HMMER3. Jobs to perform HHsearch and HHblits searches with many query profile HMMs can be parallelized over cores and over servers in a cluster using OpenMP and message passing interface (MPI).
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 (65 items)
Collapse this list.
  1. /usr/local/share/licenses/hhsuite-3.3.0_3/catalog.mk
  2. /usr/local/share/licenses/hhsuite-3.3.0_3/LICENSE
  3. /usr/local/share/licenses/hhsuite-3.3.0_3/GPLv3
  4. bin/a3m_database_extract
  5. bin/a3m_database_filter
  6. bin/a3m_database_reduce
  7. bin/a3m_extract
  8. bin/a3m_reduce
  9. bin/cstranslate
  10. bin/cstranslate_mpi
  11. bin/ffindex_apply
  12. bin/ffindex_apply_mpi
  13. bin/ffindex_build
  14. bin/ffindex_from_fasta
  15. bin/ffindex_from_fasta_with_split
  16. bin/ffindex_get
  17. bin/ffindex_modify
  18. bin/ffindex_order
  19. bin/ffindex_reduce
  20. bin/ffindex_unpack
  21. bin/hhalign
  22. bin/hhalign_mpi
  23. bin/hhalign_omp
  24. bin/hhblits
  25. bin/hhblits_ca3m
  26. bin/hhblits_mpi
  27. bin/hhblits_omp
  28. bin/hhconsensus
  29. bin/hhfilter
  30. bin/hhmake
  31. bin/hhsearch
  32. bin/hhsearch_mpi
  33. bin/hhsearch_omp
  34. share/hhsuite/data/context_data.crf
  35. share/hhsuite/data/context_data.lib
  36. share/hhsuite/data/cs219.lib
  37. share/hhsuite/data/do_not_delete
  38. share/hhsuite/data/do_not_delete.phr
  39. share/hhsuite/data/do_not_delete.pin
  40. share/hhsuite/data/do_not_delete.psq
  41. share/hhsuite/scripts/Align.pm
  42. share/hhsuite/scripts/HHPaths.pm
  43. share/hhsuite/scripts/a3m.py
  44. share/hhsuite/scripts/addss.pl
  45. share/hhsuite/scripts/check_a3m.py
  46. share/hhsuite/scripts/cif2fasta.py
  47. share/hhsuite/scripts/create_profile_from_hhm.pl
  48. share/hhsuite/scripts/create_profile_from_hmmer.pl
  49. share/hhsuite/scripts/ffindex.py
  50. share/hhsuite/scripts/get_a3m_size.py
  51. share/hhsuite/scripts/hh_reader.py
  52. share/hhsuite/scripts/hhmakemodel.pl
  53. share/hhsuite/scripts/hhmakemodel.py
  54. share/hhsuite/scripts/hhsuitedb.py
  55. share/hhsuite/scripts/mergeali.pl
  56. share/hhsuite/scripts/multithread.pl
  57. share/hhsuite/scripts/pdb2fasta.pl
  58. share/hhsuite/scripts/pdbfilter.pl
  59. share/hhsuite/scripts/pdbfilter.py
  60. share/hhsuite/scripts/reformat.pl
  61. share/hhsuite/scripts/renumberpdb.pl
  62. share/hhsuite/scripts/splitfasta.pl
  63. @owner
  64. @group
  65. @mode
Collapse this list.
Dependency lines:
  • hhsuite>0:biology/hhsuite
To install the port:
cd /usr/ports/biology/hhsuite/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/hhsuite
  • pkg install hhsuite
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: hhsuite
Flavors: there is no flavor information for this port.
NOT_FOR_ARCHS: armv6 armv7 i386 mips powerpc powerpcspe
distinfo:
TIMESTAMP = 1598500089 SHA256 (soedinglab-hh-suite-v3.3.0_GH0.tar.gz) = dd67f7f3bf601e48c9c0bc4cf1fbe3b946f787a808bde765e9436a48d27b0964 SIZE (soedinglab-hh-suite-v3.3.0_GH0.tar.gz) = 6490149
Packages (timestamps in pop-ups are UTC):
hhsuite
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest-3.3.0_3------
FreeBSD:13:quarterly-3.3.0_2------
FreeBSD:14:latest-3.3.0_3------
FreeBSD:14:quarterly-3.3.0_3------
FreeBSD:15:latest-3.3.0_3n/a-n/a---
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. cmake : devel/cmake-core
  2. ninja : devel/ninja
  3. python3.9 : lang/python39
  4. perl5>=5.36<5.37 : lang/perl5.36
Test dependencies:
  1. python3.9 : lang/python39
Runtime dependencies:
  1. python3.9 : lang/python39
  2. perl5>=5.36<5.37 : lang/perl5.36
Library dependencies:
  1. libmpi.so : net/openmpi
There are no ports dependent upon this port
Configuration Options:
No options to configure
Options name:
biology_hhsuite
USES:
compiler:c++11-lang cmake 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/soedinglab/hh-suite/tar.gz/v3.3.0?dummy=/
Collapse this list.

There are no commits on branch 2022Q2 for this port
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