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NOTE: the WWW: line in pkg-descr was relocated to a WWW= line in Makefile. Each port in FreshPorts has a homepage link. Look for it right after the Description: on each port's home page.

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The emphasis is on know, or recommended by someone I know. This is the original FreshPorts server, way past useful: RAID, 8GB RAM, etc. The drives need to be wiped and everything recycled.
Port details
abyss Assembly By Short Sequences: parallel, paired-end sequence assembler
2.3.5_1 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 Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-02-25 07:56:58
Last Update: 2022-09-07 21:58:51
Commit Hash: fb16dfe
License: GPLv3
Description:
HomepagecgitgithubgitlabSVNWeb
pkg-plist: as obtained via: make generate-plist
Expand this list (64 items)
Collapse this list.
  1. /usr/local/share/licenses/abyss-2.3.5_1/catalog.mk
  2. /usr/local/share/licenses/abyss-2.3.5_1/LICENSE
  3. /usr/local/share/licenses/abyss-2.3.5_1/GPLv3
  4. bin/ABYSS
  5. bin/ABYSS-P
  6. bin/AdjList
  7. bin/Consensus
  8. bin/DAssembler
  9. bin/DistanceEst
  10. bin/DistanceEst-ssq
  11. bin/KAligner
  12. bin/MergeContigs
  13. bin/MergePaths
  14. bin/Overlap
  15. bin/ParseAligns
  16. bin/PathConsensus
  17. bin/PathOverlap
  18. bin/PopBubbles
  19. bin/SimpleGraph
  20. bin/abyss-align
  21. bin/abyss-bloom
  22. bin/abyss-bloom-dbg
  23. bin/abyss-bloom-dist.mk
  24. bin/abyss-bowtie
  25. bin/abyss-bowtie2
  26. bin/abyss-bwa
  27. bin/abyss-bwamem
  28. bin/abyss-bwasw
  29. bin/abyss-db-csv
  30. bin/abyss-db-txt
  31. bin/abyss-dida
  32. bin/abyss-fac
  33. bin/abyss-fatoagp
  34. bin/abyss-filtergraph
  35. bin/abyss-fixmate
  36. bin/abyss-fixmate-ssq
  37. bin/abyss-gapfill
  38. bin/abyss-gc
  39. bin/abyss-index
  40. bin/abyss-junction
  41. bin/abyss-kaligner
  42. bin/abyss-layout
  43. bin/abyss-longseqdist
  44. bin/abyss-map
  45. bin/abyss-map-ssq
  46. bin/abyss-mergepairs
  47. bin/abyss-overlap
  48. bin/abyss-paired-dbg
  49. bin/abyss-paired-dbg-mpi
  50. bin/abyss-pe
  51. bin/abyss-rresolver-short
  52. bin/abyss-samtoafg
  53. bin/abyss-scaffold
  54. bin/abyss-sealer
  55. bin/abyss-stack-size
  56. bin/abyss-tabtomd
  57. bin/abyss-todot
  58. bin/abyss-tofastq
  59. bin/konnector
  60. bin/logcounter
  61. man/man1/abyss-sealer.1.gz
  62. @owner
  63. @group
  64. @mode
Collapse this list.
Dependency lines:
  • abyss>0:biology/abyss
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:
Packages (timestamps in pop-ups are UTC):
abyss
ABIlatestquarterly
FreeBSD:11:aarch64--
FreeBSD:11:amd64--
FreeBSD:11:armv6--
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64-2.3.1_1
FreeBSD:12:amd642.3.5_12.3.1_1
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i386--
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64-2.3.1_1
FreeBSD:13:amd642.3.5_12.3.1_1
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i386--
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:13:riscv64--
FreeBSD:14:aarch642.3.5_1-
FreeBSD:14:amd642.3.5_1-
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i386--
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
FreeBSD:14:riscv64--
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. version.hpp : devel/boost-libs
  2. ghc : lang/ghc
  3. pandoc : textproc/hs-pandoc
  4. gmake>=4.3 : devel/gmake
  5. autoconf>=2.71 : devel/autoconf
  6. automake>=1.16.5 : devel/automake
Runtime dependencies:
  1. bash : shells/bash
  2. gmake : devel/gmake
Library dependencies:
  1. libffi.so : devel/libffi
  2. libgmp.so : math/gmp
  3. libmpich.so : net/mpich
  4. libiconv.so : converters/libiconv
  5. libsqlite3.so : databases/sqlite3
There are no ports dependent upon this port

Configuration Options:
Options name:

USES:

FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/bcgsc/abyss/tar.gz/2.3.5?dummy=/
Collapse this list.

Number of commits found: 27

Commit History - (may be incomplete: see SVNWeb link above for full details)
CommitCreditsLog message
07 Sep 2022 21:58:51
commit 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)
2.3.5_1
07 Sep 2022 21:10:59
commit 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)
2.3.5_1
12 Aug 2022 14:46:53
commit hash:4cf39decb348615b9c8a28370d987a85d1b8a5edcommit hash:4cf39decb348615b9c8a28370d987a85d1b8a5edcommit hash:4cf39decb348615b9c8a28370d987a85d1b8a5ed files touched by this commit
Dima Panov (fluffy) search for other commits by this committer
*/*: bump all consumers after recent boost upgrade
2.3.5
30 Jul 2022 07:34:34
commit hash:5c534ae6563c43d6f99baf17f5e8b843e2da06c8commit hash:5c534ae6563c43d6f99baf17f5e8b843e2da06c8commit hash:5c534ae6563c43d6f99baf17f5e8b843e2da06c8 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/abyss: Add test target
2.3.5
29 Jul 2022 19:57:36
commit hash:0a752832a5d6a21cdbacadfa4ca6e68a7d00c7f7commit hash:0a752832a5d6a21cdbacadfa4ca6e68a7d00c7f7commit hash:0a752832a5d6a21cdbacadfa4ca6e68a7d00c7f7 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/abyss: Update 2.3.1 -> 2.3.5
2.3.1_1
09 May 2022 19:23:51
commit hash:db78da8f8b7388d951665362479eb4aa0babf1b4commit hash:db78da8f8b7388d951665362479eb4aa0babf1b4commit hash:db78da8f8b7388d951665362479eb4aa0babf1b4 files touched by this commit
Kevin Bowling (kbowling) search for other commits by this committer
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
commit hash:620968a43a5f9bb3fa98ab20f257a4c0d864caa7commit hash:620968a43a5f9bb3fa98ab20f257a4c0d864caa7commit hash:620968a43a5f9bb3fa98ab20f257a4c0d864caa7 files touched by this commit
Rene Ladan (rene) search for other commits by this committer
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
commit hash:9352bd72e0b04fdf32d9c63353aabf1a672936fdcommit hash:9352bd72e0b04fdf32d9c63353aabf1a672936fdcommit hash:9352bd72e0b04fdf32d9c63353aabf1a672936fd files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/abyss: Broken on 11

Reported by:	fallout
2.3.1
22 Apr 2021 17:18:02
commit hash:8ec7f5d3deb04932228c003c0bebfbda541bb181commit hash:8ec7f5d3deb04932228c003c0bebfbda541bb181commit hash:8ec7f5d3deb04932228c003c0bebfbda541bb181 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/abyss: Update 2.3.0-3 -> 2.3.1

Reported by:	portscout
2.3.0.3
18 Apr 2021 20:19:56
commit hash:8e65beb783c9abf477fa85e8437600b6890d94b8commit hash:8e65beb783c9abf477fa85e8437600b6890d94b8commit hash:8e65beb783c9abf477fa85e8437600b6890d94b8 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/abyss: Update 2.2.5 -> 2.3.0-3
2.2.5
07 Apr 2021 08:09:01
commit 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
2.2.5
06 Apr 2021 14:31:07
commit 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.
2.2.5
14 Mar 2021 05:17:40
Revision:568329Original commit files touched by this commit
yuri search for other commits by this committer
biology/abyss: Add PORTSCOUT line
2.2.5
27 Sep 2020 06:59:05
Revision:550242Original commit files touched by this commit
yuri search for other commits by this committer
biology/abyss: Update 2.2.4 -> 2.2.5

Reported by:	portscout
2.2.4_1
04 Jul 2020 18:11:42
Revision:541232Original commit files touched by this commit
zeising search for other commits by this committer
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
Revision:537064Original commit files touched by this commit
yuri search for other commits by this committer
biology/abyss: Update 2.2.3 -> 2.2.4
2.2.3_1
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
2.2.3
18 Jan 2020 19:46:26
Revision:523491Original commit files touched by this commit
yuri search for other commits by this committer
biology/abyss: Broken on i386

Reported by:	fallout
2.2.3
13 Jan 2020 04:06:14
Revision:522851Original commit files touched by this commit
yuri search for other commits by this committer
biology/abyss: Update 2.1.5 -> 2.2.3

Reported by:	portscout
2.1.5_6
11 Dec 2019 17:53:49
Revision:519824Original commit files touched by this commit
jbeich search for other commits by this committer
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
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/
2.1.5_4
19 Aug 2019 15:35:28
Revision:509290Original commit files touched by this commit
jbeich search for other commits by this committer
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
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
2.1.5_2
21 Jun 2019 11:43:09
Revision:504788Original commit files touched by this commit
pkubaj search for other commits by this committer
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
Revision:501030Original commit files touched by this commit
jbeich search for other commits by this committer
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
Revision:498698Original commit files touched by this commit
jbeich search for other commits by this committer
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
Revision:493842Original commit files touched by this commit
yuri search for other commits by this committer
New port: biology/abyss: Assembly By Short Sequences: parallel, paired-end
sequence assembler

Number of commits found: 27