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Port details
abyss Assembly By Short Sequences: parallel, paired-end sequence assembler
2.1.5_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
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-02-25 07:56:58
Last Update: 2019-04-12 07:36:31
SVN Revision: 498698
License: GPLv3
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.

WWW: http://www.bcgsc.ca/platform/bioinfo/software/abyss
SVNWeb : Homepage
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (63 items)
  1. /usr/local/share/licenses/abyss-2.1.5_1/catalog.mk
  2. /usr/local/share/licenses/abyss-2.1.5_1/LICENSE
  3. /usr/local/share/licenses/abyss-2.1.5_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-pe
  50. bin/abyss-samtoafg
  51. bin/abyss-samtobreak
  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. 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

There is no flavor information for this port.

distinfo:

TIMESTAMP = 1551061546
SHA256 (abyss-2.1.5.tar.gz) = 65bfc8241e6ff5adf7601ae4ae93a75e3db86d6bff5d593c75aaff7f0ef41757
SIZE (abyss-2.1.5.tar.gz) = 1201318


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
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
===> The following configuration options are available for abyss-2.1.5_1:
     DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings

USES:
gmake iconv:wchar_t localbase:ldflags shebangfix sqlite

Master Sites:
  1. http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/2.1.5/

Number of commits found: 2

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
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: 2

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