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Port details
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:latest3.3.0_3-------
FreeBSD:13:quarterly3.3.0_33.3.0_3------
FreeBSD:14:latest3.3.0_33.3.0_3------
FreeBSD:14:quarterly3.3.0_33.3.0_3------
FreeBSD:15:latest-3.3.0_3n/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.

Number of commits found: 27

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
3.3.0_3
18 Feb 2024 09:29:31
commit hash: 9eba6162f8f63de2b89ae35eef90e7c296f2373acommit hash: 9eba6162f8f63de2b89ae35eef90e7c296f2373acommit hash: 9eba6162f8f63de2b89ae35eef90e7c296f2373acommit hash: 9eba6162f8f63de2b89ae35eef90e7c296f2373a files touched by this commit
Thierry Thomas (thierry) search for other commits by this committer
*/*: bump PORTREVISION after OpenMPI upgrade
3.3.0_2
04 Feb 2024 09:24:22
commit hash: 3f54e02fce0ae99a18907aec293932c77d9a8feecommit hash: 3f54e02fce0ae99a18907aec293932c77d9a8feecommit hash: 3f54e02fce0ae99a18907aec293932c77d9a8feecommit hash: 3f54e02fce0ae99a18907aec293932c77d9a8fee files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/hhsuite: Fix build on some systems by adding missing C++ #include
statement

Reported by:	fallout
3.3.0_2
23 Apr 2023 09:09:58
commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b files touched by this commit
Gerald Pfeifer (gerald) search for other commits by this committer
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
3.3.0_1
01 Oct 2022 18:16:04
commit hash: e7cb6b0a685d45e861be55d1925b9101e88a9e64commit hash: e7cb6b0a685d45e861be55d1925b9101e88a9e64commit hash: e7cb6b0a685d45e861be55d1925b9101e88a9e64commit hash: e7cb6b0a685d45e861be55d1925b9101e88a9e64 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/hhsuite: Disable on 32-bit architectures following upstream advice
3.3.0_1
01 Oct 2022 15:08:17
commit hash: 75d814716539317715472ded1bb11b3c6ccb72bccommit hash: 75d814716539317715472ded1bb11b3c6ccb72bccommit hash: 75d814716539317715472ded1bb11b3c6ccb72bccommit hash: 75d814716539317715472ded1bb11b3c6ccb72bc files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
Author: Robert Clausecker
biology/hhsuite: fix build on armv7

PR:		266736
3.3.0_1
09 Sep 2022 21:49:50
commit hash: 65b542d259ee8de09ae6802dd2e3ed811ea8fcebcommit hash: 65b542d259ee8de09ae6802dd2e3ed811ea8fcebcommit hash: 65b542d259ee8de09ae6802dd2e3ed811ea8fcebcommit hash: 65b542d259ee8de09ae6802dd2e3ed811ea8fceb files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/hhsuite: Broken on armv7

Reported by:	fallout
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
3.3.0_1
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
3.3.0_1
04 Aug 2022 16:21:45
commit hash: efc656517495adffd7398d02ed01455f32bdf3b9commit hash: efc656517495adffd7398d02ed01455f32bdf3b9commit hash: efc656517495adffd7398d02ed01455f32bdf3b9commit hash: efc656517495adffd7398d02ed01455f32bdf3b9 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/hhsuite: Fix build on some architectures

... by removing -march=native.

Reported by:	fallout
3.3.0_1
04 Aug 2022 16:21:45
commit hash: bd8b68e6415a3671c144baa10871ef3f19f26eabcommit hash: bd8b68e6415a3671c144baa10871ef3f19f26eabcommit hash: bd8b68e6415a3671c144baa10871ef3f19f26eabcommit hash: bd8b68e6415a3671c144baa10871ef3f19f26eab files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/hhsuite: Revert commit "Broken on systems where OpenMP isn't enabled"

IT was added by mistake.
The failures on armv7 are due to -march=native.

This reverts commit 0f20e25bb0c89821c657ce7d8424f6e6ad1c9a45.

Reported by:	pkubaj@
3.3.0_1
04 Aug 2022 07:41:24
commit hash: 0f20e25bb0c89821c657ce7d8424f6e6ad1c9a45commit hash: 0f20e25bb0c89821c657ce7d8424f6e6ad1c9a45commit hash: 0f20e25bb0c89821c657ce7d8424f6e6ad1c9a45commit hash: 0f20e25bb0c89821c657ce7d8424f6e6ad1c9a45 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/hhsuite: Broken on systems where OpenMP isn't enabled

Reported by:	fallout
3.3.0_1
27 Apr 2022 13:22:04
commit hash: e7af5e32b40796da3f0c252941d5f427f7519234commit hash: e7af5e32b40796da3f0c252941d5f427f7519234commit hash: e7af5e32b40796da3f0c252941d5f427f7519234commit hash: e7af5e32b40796da3f0c252941d5f427f7519234 files touched by this commit
Piotr Kubaj (pkubaj) search for other commits by this committer
biology/hhsuite: check for omp.h on all architectures
3.3.0_1
21 Apr 2022 17:11:16
commit hash: 8a75ffbc9ffcdcf330104bfbbc95f5ad57fbf92acommit hash: 8a75ffbc9ffcdcf330104bfbbc95f5ad57fbf92acommit hash: 8a75ffbc9ffcdcf330104bfbbc95f5ad57fbf92acommit hash: 8a75ffbc9ffcdcf330104bfbbc95f5ad57fbf92a files touched by this commit
Piotr Kubaj (pkubaj) search for other commits by this committer
biology/hhsuite: drop HAVE_POWER8 on powerpc64

powerpc64 uses PPC970 as a baseline.
3.3.0
16 Nov 2021 12:03:42
commit hash: f00588c63480bbe584bbfa766e5ca86cff893cf4commit hash: f00588c63480bbe584bbfa766e5ca86cff893cf4commit hash: f00588c63480bbe584bbfa766e5ca86cff893cf4commit hash: f00588c63480bbe584bbfa766e5ca86cff893cf4 files touched by this commit
Piotr Kubaj (pkubaj) search for other commits by this committer
biology/hhsuite: fix packaging on powerpc

pkg-static: Unable to access file
/wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhalign_omp:No such
file or directory
pkg-static: Unable to access file
/wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhblits_ca3m:No such
file or directory
pkg-static: Unable to access file
/wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhblits_omp:No such
file or directory
pkg-static: Unable to access file
/wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhsearch_omp:No such
file or directory

powerpc doesn't have LLVM with libomp.
3.3.0
13 Sep 2021 15:47:57
commit hash: e9f35d7e41d9f83d4212d4fe2d2e0410a3e90f66commit hash: e9f35d7e41d9f83d4212d4fe2d2e0410a3e90f66commit hash: e9f35d7e41d9f83d4212d4fe2d2e0410a3e90f66commit hash: e9f35d7e41d9f83d4212d4fe2d2e0410a3e90f66 files touched by this commit
Mikael Urankar (mikael) search for other commits by this committer
biology/hhsuite: Fix build on aarch64

Approved by:	portmgr (build fix blanket)
3.3.0
08 Jul 2021 13:13:54
commit hash: f1475a456c8257a759010ee0b949bde85ad6ad4fcommit hash: f1475a456c8257a759010ee0b949bde85ad6ad4fcommit hash: f1475a456c8257a759010ee0b949bde85ad6ad4fcommit hash: f1475a456c8257a759010ee0b949bde85ad6ad4f files touched by this commit
Piotr Kubaj (pkubaj) search for other commits by this committer
biology/hhsuite: fix build on powerpc64*

hhsuite now supports VSX.
3.3.0
07 Apr 2021 08:09:01
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
3.3.0
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
3.3.0
27 Aug 2020 04:28:24
Revision:546314Original commit files touched by this commit
yuri search for other commits by this committer
biology/hhsuite: Update 3.2.0 -> 3.3.0

Reported by:	portscout
3.2.0_4
11 May 2020 19:33:32
Revision:534934Original commit files touched by this commit
pkubaj search for other commits by this committer
biology/hhsuite: fix build on powerpc64 elfv2

Use GCC instead of Clang:
/usr/lib/clang/10.0.0/include/mmintrin.h:216:19: error: use of undeclared
identifier '__builtin_ia32_punpckhbw'
    return (__m64)__builtin_ia32_punpckhbw((__v8qi)__m1, (__v8qi)__m2);
3.2.0_4
19 Apr 2020 09:49:02
Revision:532095Original commit files touched by this commit
danilo search for other commits by this committer
- Update net/openmpi to 4.0.3 (openmpi 1 is deprecated)
- Remove option for net/openmpi2 from science/pnetcdf (net/openmpi2 is
deprecated and will be removed)
- Fix science/gromacs plist when MPI option is enabled
- Bump PORTREVISION for all the consumers of net/openmpi
3.2.0_3
08 Mar 2020 21:56:37
Revision:528082Original commit files touched by this commit
jbeich search for other commits by this committer
Drop dependency on devel/openmp

- Drop if devel/llvm* was used as a substitute

Approved by:	yuri, rene (earlier version)
Differential Revision:	https://reviews.freebsd.org/D23020
3.2.0_2
21 Sep 2019 18:59:57
Revision:512535Original commit files touched by this commit
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/
3.2.0_1
05 Aug 2019 14:23:23
Revision:508177Original commit files touched by this commit
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
3.2.0_1
26 Jul 2019 20:46:57
Revision:507372Original commit files touched by this commit
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
3.2.0
22 May 2019 02:50:56
Revision:502244Original commit files touched by this commit
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
3.2.0
19 May 2019 06:52:39
Revision:502015Original commit files touched by this commit
yuri search for other commits by this committer
New port: biology/hhsuite: Remote protein homology detection suite

Number of commits found: 27