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Port details on branch 2022Q3
canu Single molecule 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 View this port on Repology. pkg-fallout 2.2_3Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2017-12-22 01:30:37
Last Update: 2023-07-20 17:42:34
Commit Hash: d92c080
Also Listed In: java perl5
License: GPLv2
WWW:
https://canu.readthedocs.io/
Description:
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
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (84 items)
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  1. /usr/local/share/licenses/canu-2.2_3/catalog.mk
  2. /usr/local/share/licenses/canu-2.2_3/LICENSE
  3. /usr/local/share/licenses/canu-2.2_3/GPLv2
  4. bin/alignGFA
  5. bin/bogart
  6. bin/canu
  7. bin/canu-time
  8. bin/canu.defaults
  9. bin/correctOverlaps
  10. bin/draw-tig
  11. bin/dumpBlob
  12. bin/edalign
  13. bin/errorEstimate
  14. bin/falconsense
  15. bin/filterCorrectionLayouts
  16. bin/filterCorrectionOverlaps
  17. bin/findErrors
  18. bin/findErrors-Dump
  19. bin/fixErrors
  20. bin/generateCorrectionLayouts
  21. bin/layoutReads
  22. bin/loadCorrectedReads
  23. bin/loadErates
  24. bin/loadTrimmedReads
  25. bin/mergeRanges
  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/overlapAlign
  37. bin/overlapCheck
  38. bin/overlapConvert
  39. bin/overlapImport
  40. bin/overlapInCore
  41. bin/overlapInCorePartition
  42. bin/overlapPair
  43. bin/prefixEditDistance-matchLimitGenerate
  44. bin/splitHaplotype
  45. bin/splitReads
  46. bin/sqStoreCreate
  47. bin/sqStoreDumpFASTQ
  48. bin/sqStoreDumpMetaData
  49. bin/tgStoreCompress
  50. bin/tgStoreDump
  51. bin/tgStoreLoad
  52. bin/tgTigDisplay
  53. bin/trimReads
  54. bin/utgcns
  55. lib/libcanu.a
  56. lib/perl5/site_perl/canu/Configure.pm
  57. lib/perl5/site_perl/canu/Consensus.pm
  58. lib/perl5/site_perl/canu/CorrectReads.pm
  59. lib/perl5/site_perl/canu/Defaults.pm
  60. lib/perl5/site_perl/canu/Execution.pm
  61. lib/perl5/site_perl/canu/Grid.pm
  62. lib/perl5/site_perl/canu/Grid_Cloud.pm
  63. lib/perl5/site_perl/canu/Grid_DNANexus.pm
  64. lib/perl5/site_perl/canu/Grid_LSF.pm
  65. lib/perl5/site_perl/canu/Grid_Local.pm
  66. lib/perl5/site_perl/canu/Grid_PBSTorque.pm
  67. lib/perl5/site_perl/canu/Grid_SGE.pm
  68. lib/perl5/site_perl/canu/Grid_Slurm.pm
  69. lib/perl5/site_perl/canu/HaplotypeReads.pm
  70. lib/perl5/site_perl/canu/Meryl.pm
  71. lib/perl5/site_perl/canu/Output.pm
  72. lib/perl5/site_perl/canu/OverlapBasedTrimming.pm
  73. lib/perl5/site_perl/canu/OverlapErrorAdjustment.pm
  74. lib/perl5/site_perl/canu/OverlapInCore.pm
  75. lib/perl5/site_perl/canu/OverlapMMap.pm
  76. lib/perl5/site_perl/canu/OverlapMhap.pm
  77. lib/perl5/site_perl/canu/OverlapStore.pm
  78. lib/perl5/site_perl/canu/Report.pm
  79. lib/perl5/site_perl/canu/SequenceStore.pm
  80. lib/perl5/site_perl/canu/Unitig.pm
  81. share/java/classes/mhap-2.1.3.jar
  82. @owner
  83. @group
  84. @mode
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Dependency lines:
  • canu>0:biology/canu
To install the port:
cd /usr/ports/biology/canu/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/canu
  • pkg install canu
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: canu
Flavors: there is no flavor information for this port.
NOT_FOR_ARCHS: armv6 armv7 i386 mips powerpc powerpcspe
distinfo:
TIMESTAMP = 1639774550 SHA256 (canu-2.2.tar.xz) = e4d0c7b82149114f442ccd39e18f7fe2061c63b28d53700ad896e022b73b7404 SIZE (canu-2.2.tar.xz) = 2400192

Packages (timestamps in pop-ups are UTC):
canu
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest2.2_32.2_3------
FreeBSD:13:quarterly2.2_32.2_3----2.2_32.2_3
FreeBSD:14:latest2.2_32.2_3-----2.2_2
FreeBSD:14:quarterly2.2_32.2_3----2.2_32.2_3
FreeBSD:15:latest2.2_32.2_3n/a-n/a-2.2_3-
FreeBSD:15:quarterly--n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake>=4.3 : devel/gmake
  2. perl5>=5.32.r0<5.33 : lang/perl5.32
Runtime dependencies:
  1. gnuplot : math/gnuplot
  2. java : java/openjdk8
  3. perl5>=5.32.r0<5.33 : lang/perl5.32
Library dependencies:
  1. libboost_regex.so : devel/boost-libs
There are no ports dependent upon this port

Configuration Options:
No options to configure
Options name:
biology_canu
USES:
compiler:c++11-lang gmake localbase perl5 tar:xz
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://github.com/marbl/canu/releases/download/v2.2/
Collapse this list.

There are no commits on branch 2022Q3 for this port