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Port details
canu Single molecule sequence assembler
1.6_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: 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 RSII or Oxford Nanopore MinION).

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-1.6_1/catalog.mk
  2. /usr/local/share/licenses/canu-1.6_1/LICENSE
  3. /usr/local/share/licenses/canu-1.6_1/GPLv2
  4. bin/alignGFA
  5. bin/bogart
  6. bin/bogus
  7. bin/canu
  8. bin/correctOverlaps
  9. bin/createFalconSenseInputs
  10. bin/erateEstimate
  11. bin/errorEstimate
  12. bin/estimate-mer-threshold
  13. bin/existDB
  14. bin/falcon_sense
  15. bin/fastqAnalyze
  16. bin/fastqSample
  17. bin/fastqSimulate
  18. bin/fastqSimulate-sort
  19. bin/filterCorrectionOverlaps
  20. bin/findErrors
  21. bin/findErrors-Dump
  22. bin/gatekeeperCreate
  23. bin/gatekeeperDumpFASTQ
  24. bin/gatekeeperDumpMetaData
  25. bin/gatekeeperPartition
  26. bin/generateCorrectionLayouts
  27. bin/leaff
  28. bin/maskMers
  29. bin/merTrim
  30. bin/meryl
  31. bin/mhapConvert
  32. bin/mmapConvert
  33. bin/ovStoreBucketizer
  34. bin/ovStoreBuild
  35. bin/ovStoreDump
  36. bin/ovStoreIndexer
  37. bin/ovStoreSorter
  38. bin/ovStoreStats
  39. bin/overlapConvert
  40. bin/overlapImport
  41. bin/overlapInCore
  42. bin/overlapInCorePartition
  43. bin/overlapPair
  44. bin/positionDB
  45. bin/prefixEditDistance-matchLimitGenerate
  46. bin/readConsensus
  47. bin/simple
  48. bin/splitReads
  49. bin/tgStoreCompress
  50. bin/tgStoreCoverageStat
  51. bin/tgStoreDump
  52. bin/tgStoreFilter
  53. bin/tgStoreLoad
  54. bin/tgTigDisplay
  55. bin/trimReads
  56. bin/utgcns
  57. lib/libcanu.a
  58. lib/libleaff.a
  59. lib/perl5/site_perl/canu/Configure.pm
  60. lib/perl5/site_perl/canu/Consensus.pm
  61. lib/perl5/site_perl/canu/CorrectReads.pm
  62. lib/perl5/site_perl/canu/Defaults.pm
  63. lib/perl5/site_perl/canu/ErrorEstimate.pm
  64. lib/perl5/site_perl/canu/Execution.pm
  65. lib/perl5/site_perl/canu/Gatekeeper.pm
  66. lib/perl5/site_perl/canu/Grid.pm
  67. lib/perl5/site_perl/canu/Grid_Cloud.pm
  68. lib/perl5/site_perl/canu/Grid_DNANexus.pm
  69. lib/perl5/site_perl/canu/Grid_LSF.pm
  70. lib/perl5/site_perl/canu/Grid_PBSTorque.pm
  71. lib/perl5/site_perl/canu/Grid_SGE.pm
  72. lib/perl5/site_perl/canu/Grid_Slurm.pm
  73. lib/perl5/site_perl/canu/HTML.pm
  74. lib/perl5/site_perl/canu/Meryl.pm
  75. lib/perl5/site_perl/canu/Output.pm
  76. lib/perl5/site_perl/canu/OverlapBasedTrimming.pm
  77. lib/perl5/site_perl/canu/OverlapErrorAdjustment.pm
  78. lib/perl5/site_perl/canu/OverlapInCore.pm
  79. lib/perl5/site_perl/canu/OverlapMMap.pm
  80. lib/perl5/site_perl/canu/OverlapMhap.pm
  81. lib/perl5/site_perl/canu/OverlapStore.pm
  82. lib/perl5/site_perl/canu/Report.pm
  83. lib/perl5/site_perl/canu/Unitig.pm
  84. share/java/classes/mhap-2.1.2.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 = 1507077399
SHA256 (marbl-canu-v1.6_GH0.tar.gz) = 470e0ac761d69d1fecab85da810a6474b1e2387d7124290a0e4124d660766498
SIZE (marbl-canu-v1.6_GH0.tar.gz) = 2486338


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

Build dependencies:
  1. gmake : devel/gmake
  2. perl5>=5.24<5.25 : lang/perl5.24
Runtime dependencies:
  1. gnuplot : math/gnuplot
  2. java : java/openjdk8
  3. perl5>=5.24<5.25 : lang/perl5.24
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/v1.6?dummy=/

Number of commits found: 3

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
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: 3

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