Port details |
- abyss Assembly By Short Sequences: parallel, paired-end sequence assembler
- 2.3.10 biology =2 2.3.9Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2019-02-25 07:56:58
- Last Update: 2024-11-04 20:36:54
- Commit Hash: 41b83c53
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: GPLv3
- WWW:
- https://www.bcgsc.ca/resources/software/abyss/
- Description:
- ABySS is a de novo, parallel, paired-end sequence assembler that is designed for
short reads. The single-processor version is useful for assembling genomes up to
100 Mbases in size. The parallel version is implemented using MPI and is capable
of assembling larger genomes.
- ¦ ¦ ¦ ¦
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- To install the port:
- cd /usr/ports/biology/abyss/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/abyss
- pkg install abyss
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: abyss
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1730727252
SHA256 (bcgsc-abyss-2.3.10_GH0.tar.gz) = 08ff30002113280ae75228eb1e29cf835318c7ef783ccf24fbe7350d49b4043c
SIZE (bcgsc-abyss-2.3.10_GH0.tar.gz) = 1323490
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:
-
- version.hpp : devel/boost-libs
- ghc : lang/ghc
- pandoc : textproc/hs-pandoc
- gmake>=4.4.1 : devel/gmake
- autoconf>=2.72 : devel/autoconf
- automake>=1.17 : devel/automake
- Runtime dependencies:
-
- bash : shells/bash
- gmake : devel/gmake
- Library dependencies:
-
- libbtllib.so : biology/btllib
- libffi.so : devel/libffi
- libgmp.so : math/gmp
- libmpich.so : net/mpich
- libiconv.so : converters/libiconv
- libsqlite3.so : databases/sqlite3
- There are no ports dependent upon this port
Configuration Options:
- ===> The following configuration options are available for abyss-2.3.10:
DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings
- Options name:
- biology_abyss
- USES:
- autoreconf compiler:c++11-lang gmake iconv:wchar_t localbase:ldflags shebangfix sqlite
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
Commit | Credits | Log message |
2.3.10 04 Nov 2024 20:36:54 |
Yuri Victorovich (yuri) Author: Älven |
biology/abyss: update 2.3.9 → 2.3.10
PR: 282540 |
2.3.9 01 Oct 2024 18:56:20 |
Rene Ladan (rene) |
all: drop support for expired FreeBSD 14.0
Simplify expressions for FreeBSD 13.X
Reviewed by: many
Differential Revision: https://reviews.freebsd.org/D46601 |
2.3.9 12 Sep 2024 09:18:11 |
Yuri Victorovich (yuri) |
biology/abyss: update 2.3.8 → 2.3.9
Reported by: portscout |
2.3.8 23 Jul 2024 00:34:22 |
Yuri Victorovich (yuri) |
biology/abyss: update 2.3.7 → 2.3.8
Reported by: portscout |
2.3.7_2 03 Mar 2024 10:04:08 |
Nuno Teixeira (eduardo) |
biology/abyss: Move man pages to share/man
Approved by: portmgr (blanket) |
2.3.7_1 10 Dec 2023 10:23:11 |
Thierry Thomas (thierry) |
*/*: bump PORTREVISION after the upgrade of MPICH to 4.1.2 |
2.3.7 22 Jul 2023 08:55:01 |
Yuri Victorovich (yuri) |
biology/abyss: Update 2.3.5 → 2.3.7
Reported by: portscout |
2.3.5_2 07 Jun 2023 07:25:09 |
Muhammad Moinur Rahman (bofh) |
biology/abyss: Fix build with llvm15
Approved by: portmgr (blanket) |
2.3.5_2 23 Apr 2023 09:09:58 |
Gerald Pfeifer (gerald) |
*: Bump PORTREVISIONs for math/mpc update to 1.3.1 |
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) |
2.3.5_1 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 ) |
2.3.5_1 12 Aug 2022 14:46:53 |
Dima Panov (fluffy) |
*/*: bump all consumers after recent boost upgrade |
2.3.5 30 Jul 2022 07:34:34 |
Yuri Victorovich (yuri) |
biology/abyss: Add test target |
2.3.5 29 Jul 2022 19:57:36 |
Yuri Victorovich (yuri) |
biology/abyss: Update 2.3.1 -> 2.3.5 |
2.3.1_1 09 May 2022 19:23:51 |
Kevin Bowling (kbowling) |
devel/libffi: Bump deps PORTREVISION for shlib change
PR: 263764
Reported by: VVD <vvd@unislabs.com> |
2.3.1 30 Sep 2021 21:23:30 |
Rene Ladan (rene) |
cleanup: drop support for EOL FreeBSD 11.X
Search criteria used:
- 11.4
- OSREL*
- OSVER*
- *_FreeBSD_11
Input from:
- adridg: devel/qca-legacy
- jbeich: _WITH_DPRINTF, _WITH_GETLINE, GNU bfd workarounds
- sunpoet: security/p5-*OpenSSL*
Reviewed by: doceng, kde, multimedia, perl, python, ruby, rust
Differential Revision: https://reviews.freebsd.org/D32008
Test Plan: make index |
2.3.1 21 Aug 2021 19:02:36 |
Yuri Victorovich (yuri) |
biology/abyss: Broken on 11
Reported by: fallout |
2.3.1 22 Apr 2021 17:18:02 |
Yuri Victorovich (yuri) |
biology/abyss: Update 2.3.0-3 -> 2.3.1
Reported by: portscout |
2.3.0.3 18 Apr 2021 20:19:56 |
Yuri Victorovich (yuri) |
biology/abyss: Update 2.2.5 -> 2.3.0-3 |
2.2.5 07 Apr 2021 08:09:01 |
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
2.2.5 06 Apr 2021 14:31:07 |
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
2.2.5 14 Mar 2021 05:17:40 |
yuri |
biology/abyss: Add PORTSCOUT line |
2.2.5 27 Sep 2020 06:59:05 |
yuri |
biology/abyss: Update 2.2.4 -> 2.2.5
Reported by: portscout |
2.2.4_1 04 Jul 2020 18:11:42 |
zeising |
Chanse update of devel/libffi
Chase the devel/libffi update
Bump portrevision of all dependent ports to chace shard library version bump
in libffi.
Update LIB_DEPENDS lines where needed to not require a specific version of
libffi.so.
PR: 247028 (for tracking) |
2.2.4 30 May 2020 09:10:44 |
yuri |
biology/abyss: Update 2.2.3 -> 2.2.4 |
2.2.3_1 08 Mar 2020 21:56:37 |
jbeich |
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 |
2.2.3 18 Jan 2020 19:46:26 |
yuri |
biology/abyss: Broken on i386
Reported by: fallout |
2.2.3 13 Jan 2020 04:06:14 |
yuri |
biology/abyss: Update 2.1.5 -> 2.2.3
Reported by: portscout |
2.1.5_6 11 Dec 2019 17:53:49 |
jbeich |
devel/boost-*: update to 1.72.0
Changes: http://www.boost.org/users/history/version_1_72_0.html
PR: 241449
Exp-run by: antoine
Differential Revision: https://reviews.freebsd.org/D22136 |
2.1.5_5 21 Sep 2019 18:59:57 |
jbeich |
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/ |
2.1.5_4 19 Aug 2019 15:35:28 |
jbeich |
devel/boost-*: update to 1.71.0
Changes: http://www.boost.org/users/history/version_1_71_0.html
PR: 238827
Exp-run by: antoine
Differential Revision: https://reviews.freebsd.org/D20774 |
2.1.5_3 26 Jul 2019 20:46:57 |
gerald |
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 |
2.1.5_2 21 Jun 2019 11:43:09 |
pkubaj |
biology/abyss: fix build on big-endian architectures
Use new GCC from ports on GCC architectures.
Merge 25eb9d2a914fb211fdfe04fcda5593f29fd23ff5, fixes build on GCC
architectures.
Also include sys/endian.h and use bswap32 and bswap64 for byte-swapping (PR at
https://github.com/bcgsc/abyss/pull/287 ).
PR: 238737
Approved by: yuri (maintainer), mat (mentor)
Differential Revision: https://reviews.freebsd.org/D20717 |
2.1.5_2 08 May 2019 16:05:53 |
jbeich |
devel/openmp: phase out
- Expire after the last version without /usr/lib/libomp.so
- Drop SOVERSION for seamless transition (i.e., avoid conditionals)
PR: 236907
Approved by: bapt (maintainer)
Differential Revision: https://reviews.freebsd.org/D19767 |
2.1.5_1 12 Apr 2019 06:36:31 |
jbeich |
devel/boost-*: update to 1.70.0
Changes: http://www.boost.org/users/history/version_1_70_0.html
PR: 235956
Exp-run by: antoine
Differential Revision: https://reviews.freebsd.org/D19303 |
2.1.5 25 Feb 2019 07:56:45 |
yuri |
New port: biology/abyss: Assembly By Short Sequences: parallel, paired-end
sequence assembler |