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Port details
canu Single molecule sequence assembler
1.8 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: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 22 Dec 2017 01:30:37
Also Listed In: java perl5
License: GPLv2
Canu is a fork of the Celera Assembler, designed for high-noise single-molecule
sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).

Canu is a hierarchical assembly pipeline which runs in four steps:

    Detect overlaps in high-noise sequences using MHAP

    Generate corrected sequence consensus

    Trim corrected sequences

    Assemble trimmed corrected sequences

WWW: http://canu.readthedocs.io/
SVNWeb : Homepage : PortsMon
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (84 items)
  1. /usr/local/share/licenses/canu-1.8/catalog.mk
  2. /usr/local/share/licenses/canu-1.8/LICENSE
  3. /usr/local/share/licenses/canu-1.8/GPLv2
  4. bin/alignGFA
  5. bin/bogart
  6. bin/bogus
  7. bin/canu
  8. bin/canu.defaults
  9. bin/correctOverlaps
  10. bin/dumpBlob
  11. bin/edalign
  12. bin/errorEstimate
  13. bin/falconsense
  14. bin/fastqAnalyze
  15. bin/fastqSample
  16. bin/fastqSimulate
  17. bin/fastqSimulate-sort
  18. bin/filterCorrectionLayouts
  19. bin/filterCorrectionOverlaps
  20. bin/findErrors
  21. bin/findErrors-Dump
  22. bin/generateCorrectionLayouts
  23. bin/loadCorrectedReads
  24. bin/loadErates
  25. bin/loadTrimmedReads
  26. bin/meryl
  27. bin/mhapConvert
  28. bin/mmapConvert
  29. bin/ovStoreBucketizer
  30. bin/ovStoreBuild
  31. bin/ovStoreConfig
  32. bin/ovStoreDump
  33. bin/ovStoreIndexer
  34. bin/ovStoreSorter
  35. bin/ovStoreStats
  36. bin/overlapConvert
  37. bin/overlapImport
  38. bin/overlapInCore
  39. bin/overlapInCorePartition
  40. bin/overlapPair
  41. bin/prefixEditDistance-matchLimitGenerate
  42. bin/readConsensus
  43. bin/sequence
  44. bin/splitHaplotype
  45. bin/splitReads
  46. bin/sqStoreCreate
  47. bin/sqStoreCreatePartition
  48. bin/sqStoreDumpFASTQ
  49. bin/sqStoreDumpMetaData
  50. bin/tgStoreCompress
  51. bin/tgStoreCoverageStat
  52. bin/tgStoreDump
  53. bin/tgStoreFilter
  54. bin/tgStoreLoad
  55. bin/tgTigDisplay
  56. bin/trimReads
  57. bin/utgcns
  58. bin/wtdbgConvert
  59. lib/libcanu.a
  60. lib/perl5/site_perl/canu/Configure.pm
  61. lib/perl5/site_perl/canu/Consensus.pm
  62. lib/perl5/site_perl/canu/CorrectReads.pm
  63. lib/perl5/site_perl/canu/Defaults.pm
  64. lib/perl5/site_perl/canu/Execution.pm
  65. lib/perl5/site_perl/canu/Grid.pm
  66. lib/perl5/site_perl/canu/Grid_Cloud.pm
  67. lib/perl5/site_perl/canu/Grid_DNANexus.pm
  68. lib/perl5/site_perl/canu/Grid_LSF.pm
  69. lib/perl5/site_perl/canu/Grid_PBSTorque.pm
  70. lib/perl5/site_perl/canu/Grid_SGE.pm
  71. lib/perl5/site_perl/canu/Grid_Slurm.pm
  72. lib/perl5/site_perl/canu/HaplotypeReads.pm
  73. lib/perl5/site_perl/canu/Meryl.pm
  74. lib/perl5/site_perl/canu/Output.pm
  75. lib/perl5/site_perl/canu/OverlapBasedTrimming.pm
  76. lib/perl5/site_perl/canu/OverlapErrorAdjustment.pm
  77. lib/perl5/site_perl/canu/OverlapInCore.pm
  78. lib/perl5/site_perl/canu/OverlapMMap.pm
  79. lib/perl5/site_perl/canu/OverlapMhap.pm
  80. lib/perl5/site_perl/canu/OverlapStore.pm
  81. lib/perl5/site_perl/canu/Report.pm
  82. lib/perl5/site_perl/canu/SequenceStore.pm
  83. lib/perl5/site_perl/canu/Unitig.pm
  84. share/java/classes/mhap-2.1.3.jar
  85. Collapse this list.

To install the port: cd /usr/ports/biology/canu/ && make install clean
To add the package: pkg install canu

PKGNAME: canu

distinfo:

TIMESTAMP = 1540317173
SHA256 (marbl-canu-v1.8_GH0.tar.gz) = 30ecfe574166f54f79606038830f68927cf0efab33bdc3c6e43fd1448fa0b2e4
SIZE (marbl-canu-v1.8_GH0.tar.gz) = 2465314


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. gmake : devel/gmake
  2. perl5>=5.26<5.27 : lang/perl5.26
Runtime dependencies:
  1. gnuplot : math/gnuplot
  2. java : java/openjdk8
  3. perl5>=5.26<5.27 : lang/perl5.26
Library dependencies:
  1. libboost_regex.so : devel/boost-libs
There are no ports dependent upon this port

Configuration Options
     No options to configure

USES:
compiler:openmp gmake perl5

Master Sites:
  1. https://codeload.github.com/marbl/canu/tar.gz/v1.8?dummy=/

Number of commits found: 10

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
04 Nov 2018 14:29:03
Original commit files touched by this commit  1.8
Revision:484077
jwb search for other commits by this committer
biology/canu: Upgrade to 1.8, add experimental SLURM integration

Solves build issue with gcc8.

PR:             232930
Reported by:    gerald
Approved by:    jrm (mentor, implicit)
09 Aug 2018 06:58:31
Original commit files touched by this commit  1.7_2
Revision:476723
jbeich search for other commits by this committer
devel/boost-*: update to 1.68.0

- Switch to C++14 for libboost_system to support C++14 consumers

Changes:	http://www.boost.org/users/history/version_1_68_0.html
PR:		229569
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D16165
29 Jul 2018 22:18:46
Original commit files touched by this commit  1.7_1
Revision:475857
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
in the ports tree (via Mk/bsd.default-versions.mk and lang/gcc) which
has now moved from GCC 6 to GCC 7 by default.

This includes ports
 - featuring USE_GCC=yes or USE_GCC=any,
 - featuring USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and those
 - with USES=compiler specifying one of openmp, nestedfct, c11, c++0x,
   c++11-lib, c++11-lang, c++14-lang, c++17-lang, or gcc-c++11-lib.

PR:		222542
21 Jun 2018 23:52:37
Original commit files touched by this commit  1.7
Revision:473009
linimon search for other commits by this committer
Mark as broken on aarch64, and, where appropriate, armvX.

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)
26 Apr 2018 04:16:15
Original commit files touched by this commit  1.7
Revision:468321
jwb search for other commits by this committer
biology/canu: Upgrade to 1.7 release

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15201
18 Apr 2018 13:57:43
Original commit files touched by this commit  1.6_3
Revision:467711
jbeich search for other commits by this committer
devel/boost-*: update to 1.67.0

Changes:	http://www.boost.org/users/history/version_1_67_0.html
PR:		227427
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D15030
10 Mar 2018 17:46:06
Original commit files touched by this commit  1.6_2
Revision:464084
gerald search for other commits by this committer
Bump PORTREVISIONs of all users of math/mpc that we just updated to
version 1.1.0 (via revision 464079).
18 Jan 2018 04:11:03
Original commit files touched by this commit  1.6_1
Revision:459315
jbeich search for other commits by this committer
devel/boost-*: update to 1.66.0

Changes:	http://www.boost.org/users/history/version_1_66_0.html
PR:		223922
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D13279
22 Dec 2017 14:14:11
Original commit files touched by this commit  1.6
Revision:456982
jwb search for other commits by this committer
biology/canu: Replace += with = for depends

Approved by:    jrm
Differential Revision:  https://reviews.freebsd.org/D13574
22 Dec 2017 01:30:27
Original commit files touched by this commit  1.6
Revision:456950
jwb search for other commits by this committer
[new port] biology/canu: Single molecule sequence assembler

Approved by: jrm (mentor) or wen (mentor)
Differential Revision:  https://reviews.freebsd.org/D13574

Number of commits found: 10

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