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Port details
abyss Assembly By Short Sequences: parallel, paired-end sequence assembler
2.2.3 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 2.1.5Version 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: 2020-01-18 19:46:26
SVN Revision: 523491
License: GPLv3
Description:
SVNWeb : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (62 items)
  1. /usr/local/share/licenses/abyss-2.2.3/catalog.mk
  2. /usr/local/share/licenses/abyss-2.2.3/LICENSE
  3. /usr/local/share/licenses/abyss-2.2.3/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-samtoafg
  51. bin/abyss-scaffold
  52. bin/abyss-sealer
  53. bin/abyss-stack-size
  54. bin/abyss-tabtomd
  55. bin/abyss-todot
  56. bin/abyss-tofastq
  57. bin/konnector
  58. bin/logcounter
  59. man/man1/ABYSS.1.gz
  60. man/man1/abyss-pe.1.gz
  61. man/man1/abyss-sealer.1.gz
  62. man/man1/abyss-tofastq.1.gz
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: pkg install abyss
PKGNAME: abyss
Flavors: there is no flavor information for this port.
distinfo:

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 : 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. libomp.so : devel/openmp
  4. libiconv.so : converters/libiconv
  5. libsqlite3.so : databases/sqlite3
There are no ports dependent upon this port

Configuration Options

USES:

Master Sites:
  1. https://codeload.github.com/bcgsc/abyss/tar.gz/2.2.3?dummy=/

Number of commits found: 10

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
18 Jan 2020 19:46:26
Original commit files touched by this commit  2.2.3
Revision:523491
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  2.2.3
Revision:522851
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  2.1.5_6
Revision:519824
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  2.1.5_5
Revision:512535
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  2.1.5_4
Revision:509290
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  2.1.5_3
Revision:507372
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  2.1.5_2
Revision:504788
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  2.1.5_2
Revision:501030
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  2.1.5_1
Revision:498698
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  2.1.5
Revision:493842
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: 10

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