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Port details
hhsuite Remote protein homology detection suite
3.2.0_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 3.2.0Version 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: 2019-09-21 19:59:57
SVN Revision: 512535
Also Listed In: science
License: GPLv3
Description:
SVNWeb : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (62 items)
  1. /usr/local/share/licenses/hhsuite-3.2.0_2/catalog.mk
  2. /usr/local/share/licenses/hhsuite-3.2.0_2/LICENSE
  3. /usr/local/share/licenses/hhsuite-3.2.0_2/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
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: pkg install hhsuite
PKGNAME: hhsuite
Flavors: there is no flavor information for this port.
distinfo:

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. openmpi>0 : net/openmpi
  2. cmake : devel/cmake
  3. ninja : devel/ninja
  4. python3.6 : lang/python36
  5. perl5>=5.30.r1<5.31 : lang/perl5.30
Runtime dependencies:
  1. openmpi>0 : net/openmpi
  2. python3.6 : lang/python36
  3. perl5>=5.30.r1<5.31 : lang/perl5.30
Library dependencies:
  1. libomp.so : devel/openmp
There are no ports dependent upon this port

Configuration Options

USES:

Master Sites:
  1. https://codeload.github.com/soedinglab/hh-suite/tar.gz/v3.2.0?dummy=/

Number of commits found: 5

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
21 Sep 2019 18:59:57
Original commit files touched by this commit  3.2.0_2
Revision:512535
jbeich search for other commits by this committer
devel/openmp: update to 9.0.0

- Connect tests to the framework to help QA remaining patches
- Force rebuild all consumers after https://reviews.llvm.org/D59783

Changes:	http://llvm.org/viewvc/llvm-project/openmp/tags/RELEASE_900/final/?view=log
ABI:		https://abi-laboratory.pro/tracker/timeline/llvm_openmp/
05 Aug 2019 14:23:23
Original commit files touched by this commit  3.2.0_1
Revision:508177
pkubaj search for other commits by this committer
biology/hhsuite: fix build on powerpc64

This port can't use Altivec. Instead, it's possible to use GCC's translation
layer from SSE. Adjust build flags to do it.

PR:		239645
Approved by:	yuri (maintainer), tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D21160
26 Jul 2019 20:46:57
Original commit files touched by this commit  3.2.0_1
Revision:507372
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330
22 May 2019 02:50:56
Original commit files touched by this commit  3.2.0
Revision:502244
yuri search for other commits by this committer
biology/hhsuite: Fix build on platforms where SIMD instruction set doesn't exist
or isn't detected.

It forces it to default to SSE2 on amd64/i386 and relaxes the SIMD requirement
on all other platforms.

Reported by:	fallout
19 May 2019 06:52:39
Original commit files touched by this commit  3.2.0
Revision:502015
yuri search for other commits by this committer
New port: biology/hhsuite: Remote protein homology detection suite

Number of commits found: 5

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