| Port details |
- mmseqs2 Ultra fast and sensitive sequence search and clustering suite
- 17.b804.f biology
 =2      13.45111_2Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2021-06-24 17:33:13
- Last Update: 2025-01-25 13:24:31
- Commit Hash: 2889989
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: GPLv3
- WWW:
- https://github.com/soedinglab/MMseqs2/
- Description:
- MMseqs2 (Many-against-Many searching) is a software suite to search
and cluster huge sequence sets. MMseqs2 is designed to run on multiple
cores and servers, making it highly scalable. MMseqs2 matches the
sensitivity of BLAST, but runs orders of magnitude faster.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- MMseqs2>0:biology/mmseqs2
- To install the port:
- cd /usr/ports/biology/mmseqs2/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/mmseqs2
- pkg install MMseqs2
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: MMseqs2
- Flavors: there is no flavor information for this port.
- NOT_FOR_ARCHS: armv6 armv7 i386 mips powerpc powerpcspe
- distinfo:
- TIMESTAMP = 1737298121
SHA256 (soedinglab-MMseqs2-17-b804f_GH0.tar.gz) = 300ebd14bf4e007b339037e5f73d8ff9c4e34f8495204c4a8c59c7672b689db2
SIZE (soedinglab-MMseqs2-17-b804f_GH0.tar.gz) = 13364452
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- zstd>0 : archivers/zstd
- cmake : devel/cmake-core
- ninja : devel/ninja
- perl5>=5.36<5.37 : lang/perl5.36
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- biology_mmseqs2
- USES:
- cmake perl5 shebangfix
- pkg-message:
- For install:
-
MMseqs2 can benefit greatly from advanced CPU features such as AVX.
Consider setting additional optimizations such as -march=native (e.g.
in make.conf) and reinstalling from source via
cd ${PORTSDIR}/biology/mmseqs2 && make install
- Master Sites:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
17.b804.f
25 Jan 2025 13:24:31
 |
Jason W. Bacon (jwb) |
biology/mmseqs2: Update to 17.b804.f
MMseqs2 Release 17 is mostly a bug fix release. Highlights include
usability improvements in MMseqs2-GPU and fix for a common crash in
the prefilter that was affecting many clustering runs.
Changes: https://github.com/soedinglab/MMseqs2/releases
PR: 284165
Reported by: alster@vinterdalen.se |
16.747.c6
15 Jan 2025 15:06:03
|
Jason W. Bacon (jwb) |
biology/mmseqs2: Update to 16.747.c6
Numerous fixes and improvements since v13
Changes: https://github.com/soedinglab/MMseqs2/releases
PR: 283251
Reported by: alster@vinterdalen.se |
07 Sep 2022 21:58:51
|
Stefan Eßer (se) |
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) |
13.45111_2
07 Sep 2022 21:10:59
|
Stefan Eßer (se) |
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  ) |
13.45111_2
23 Jul 2022 16:40:43
|
Yuri Victorovich (yuri) |
biology/mmseqs2: Not require OpenMP on systems where OpenMP isn't enabled
Reported by: fallout
Approved by: portmgr (blanket) |
13.45111_2
12 Sep 2021 21:05:53
|
Piotr Kubaj (pkubaj) |
biology/mmseqs2: disable on 32-bits
32-bits are not supported per https://github.com/soedinglab/MMseqs2/issues/460 |
13.45111_2
29 Jun 2021 14:04:48
|
Jason W. Bacon (jwb) |
biology/mmseqs2: Fix runtime error when built with clang
Disable IPS4O to avoid deadlocks (upstream developer fix)
Removing USE_GCC should fix pkg build errors caused by |
13.45111_1
26 Jun 2021 16:29:25
|
Jason W. Bacon (jwb) |
biology/mmseqs2: Enable at least SSE2 by default
Hangs when built with clang and minimal optimizations, so build with
GCC temporarily. Upstream is investigating. |
13.45111
24 Jun 2021 17:31:42
|
Jason W. Bacon (jwb) |
biology/mmseqs2: Ultra fast and sensitive sequence search and clustering suite
MMseqs2 (Many-against-Many sequence searching) is a software suite to search
and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source
GPL-licensed software implemented in C++ for FreeBSD, Linux, MacOS, and (via
via cygwin) Windows. The software is designed to run on multiple cores and
servers and exhibits very good scalability. MMseqs2 can run 10000 times
faster than BLAST. At 100 times its speed it achieves almost the same
sensitivity. It can perform profile searches with the same sensitivity as
PSI-BLAST at over 400 times its speed. |
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