notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)
Port details
abyss Assembly By Short Sequences: parallel, paired-end sequence assembler
2.3.1 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 2.2.5Version 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: 2021-04-22 17:18:02
Commit Hash: 8ec7f5d
License: GPLv3
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (66 items)
Collapse this list.
  1. /usr/local/share/licenses/abyss-2.3.1/catalog.mk
  2. /usr/local/share/licenses/abyss-2.3.1/LICENSE
  3. /usr/local/share/licenses/abyss-2.3.1/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-pe
  50. bin/abyss-rresolver-short
  51. bin/abyss-samtoafg
  52. bin/abyss-scaffold
  53. bin/abyss-sealer
  54. bin/abyss-stack-size
  55. bin/abyss-tabtomd
  56. bin/abyss-todot
  57. bin/abyss-tofastq
  58. bin/konnector
  59. bin/logcounter
  60. man/man1/ABYSS.1.gz
  61. man/man1/abyss-pe.1.gz
  62. man/man1/abyss-sealer.1.gz
  63. man/man1/abyss-tofastq.1.gz
  64. @owner
  65. @group
  66. @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
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:amd64-2.2.5
FreeBSD:11:armv6--
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64-2.2.5
FreeBSD:12:amd642.3.12.2.5
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i386--
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64-2.2.5
FreeBSD:13:amd642.3.12.2.5
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i386--
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:14:aarch642.3.1-
FreeBSD:14:amd642.3.1-
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i386--
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
 

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>=2.69 : devel/autoconf
  6. automake>=1.16.1 : 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. libiconv.so : converters/libiconv
  4. libsqlite3.so : databases/sqlite3
There are no ports dependent upon this port

Configuration Options:
Options name:

USES:

Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/bcgsc/abyss/tar.gz/2.3.1?dummy=/
Collapse this list.

Number of commits found: 19

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
22 Apr 2021 17:18:02
 files touched by this commit commit hash:8ec7f5d3deb04932228c003c0bebfbda541bb181  2.3.1
yuri search for other commits by this committer
biology/abyss: Update 2.3.0-3 -> 2.3.1

Reported by:	portscout
18 Apr 2021 20:19:56
 files touched by this commit commit hash:8e65beb783c9abf477fa85e8437600b6890d94b8  2.3.0.3
yuri search for other commits by this committer
biology/abyss: Update 2.2.5 -> 2.3.0-3
07 Apr 2021 08:09:01
 files touched by this commit commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  2.2.5
mat search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
06 Apr 2021 14:31:07
 files touched by this commit commit hash:305f148f482daf30dcf728039d03d019f88344eb  2.2.5
mat search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
14 Mar 2021 05:17:40
Original commit files touched by this commit Revision:568329  2.2.5
yuri search for other commits by this committer
biology/abyss: Add PORTSCOUT line
27 Sep 2020 06:59:05
Original commit files touched by this commit Revision:550242  2.2.5
yuri search for other commits by this committer
biology/abyss: Update 2.2.4 -> 2.2.5

Reported by:	portscout
04 Jul 2020 18:11:42
Original commit files touched by this commit Revision:541232  2.2.4_1
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)
30 May 2020 09:10:44
Original commit files touched by this commit Revision:537064  2.2.4
yuri search for other commits by this committer
biology/abyss: Update 2.2.3 -> 2.2.4
08 Mar 2020 21:56:37
Original commit files touched by this commit Revision:528082  2.2.3_1
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
18 Jan 2020 19:46:26
Original commit files touched by this commit Revision:523491  2.2.3
yuri search for other commits by this committer
biology/abyss: Broken on i386

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

Reported by:	portscout
11 Dec 2019 17:53:49
Original commit files touched by this commit Revision:519824  2.1.5_6
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
21 Sep 2019 18:59:57
Original commit files touched by this commit Revision:512535  2.1.5_5
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/
19 Aug 2019 15:35:28
Original commit files touched by this commit Revision:509290  2.1.5_4
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
26 Jul 2019 20:46:57
Original commit files touched by this commit Revision:507372  2.1.5_3
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
21 Jun 2019 11:43:09
Original commit files touched by this commit Revision:504788  2.1.5_2
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
08 May 2019 16:05:53
Original commit files touched by this commit Revision:501030  2.1.5_2
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
12 Apr 2019 06:36:31
Original commit files touched by this commit Revision:498698  2.1.5_1
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
25 Feb 2019 07:56:45
Original commit files touched by this commit Revision:493842  2.1.5
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: 19