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Port details
canu Single molecule sequence assembler
2.1_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 View this port on Repology. pkg-fallout 2.1_1Version 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: 2021-04-07 08:09:01
Commit Hash: cf118cc
Also Listed In: java perl5
License: GPLv2
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (83 items)
Collapse this list.
  1. /usr/local/share/licenses/canu-2.1_1/catalog.mk
  2. /usr/local/share/licenses/canu-2.1_1/LICENSE
  3. /usr/local/share/licenses/canu-2.1_1/GPLv2
  4. bin/alignGFA
  5. bin/bogart
  6. bin/bogus
  7. bin/canu
  8. bin/canu-time
  9. bin/canu.defaults
  10. bin/correctOverlaps
  11. bin/draw-tig
  12. bin/dumpBlob
  13. bin/edalign
  14. bin/errorEstimate
  15. bin/falconsense
  16. bin/filterCorrectionLayouts
  17. bin/filterCorrectionOverlaps
  18. bin/findErrors
  19. bin/findErrors-Dump
  20. bin/fixErrors
  21. bin/generateCorrectionLayouts
  22. bin/layoutReads
  23. bin/loadCorrectedReads
  24. bin/loadErates
  25. bin/loadTrimmedReads
  26. bin/mergeRanges
  27. bin/meryl
  28. bin/mhapConvert
  29. bin/mmapConvert
  30. bin/ovStoreBucketizer
  31. bin/ovStoreBuild
  32. bin/ovStoreConfig
  33. bin/ovStoreDump
  34. bin/ovStoreIndexer
  35. bin/ovStoreSorter
  36. bin/ovStoreStats
  37. bin/overlapAlign
  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_PBSTorque.pm
  66. lib/perl5/site_perl/canu/Grid_SGE.pm
  67. lib/perl5/site_perl/canu/Grid_Slurm.pm
  68. lib/perl5/site_perl/canu/HaplotypeReads.pm
  69. lib/perl5/site_perl/canu/Meryl.pm
  70. lib/perl5/site_perl/canu/Output.pm
  71. lib/perl5/site_perl/canu/OverlapBasedTrimming.pm
  72. lib/perl5/site_perl/canu/OverlapErrorAdjustment.pm
  73. lib/perl5/site_perl/canu/OverlapInCore.pm
  74. lib/perl5/site_perl/canu/OverlapMMap.pm
  75. lib/perl5/site_perl/canu/OverlapMhap.pm
  76. lib/perl5/site_perl/canu/OverlapStore.pm
  77. lib/perl5/site_perl/canu/Report.pm
  78. lib/perl5/site_perl/canu/SequenceStore.pm
  79. lib/perl5/site_perl/canu/Unitig.pm
  80. share/java/classes/mhap-2.1.3.jar
  81. @owner
  82. @group
  83. @mode
Collapse this list.
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
PKGNAME: canu
Flavors: there is no flavor information for this port.
NOT_FOR_ARCHS: armv6 armv7 i386 powerpc
distinfo:
Packages (timestamps in pop-ups are UTC):
canu
ABIlatestquarterly
FreeBSD:11:aarch64--
FreeBSD:11:amd642.1_12.1_1
FreeBSD:11:armv6--
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64--
FreeBSD:12:amd642.1_12.1_1
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i386--
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64--
FreeBSD:13:amd642.1_12.1_1
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i386--
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:14:aarch64--
FreeBSD:14:amd642.1_1-
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i386--
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
 

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:
Options name:

USES:

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/v2.1/
Collapse this list.

Number of commits found: 25

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
07 Apr 2021 08:09:01
 files touched by this commit commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  2.1_1
mat search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
06 Apr 2021 14:31:07
 files touched by this commit commit hash:305f148f482daf30dcf728039d03d019f88344eb  2.1_1
mat search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
11 Jan 2021 16:51:16
Original commit files touched by this commit Revision:561227  2.1_1
jwb search for other commits by this committer
biology/canu: Drop dependency on gcc

Replace compiler:openmp with compiler:c++11-lang and localbase

PR:             port/247753, ports/252379
14 Sep 2020 22:27:37
Original commit files touched by this commit Revision:548685  2.1
jwb search for other commits by this committer
biology/canu: Upgrade to 2.1

Numerous functional improvements for ease of use and output quality
A few bug fixes

Reported by:    portscout
17 May 2020 02:25:17
Original commit files touched by this commit Revision:535507  2.0
linimon search for other commits by this committer
Mark as BROKEN on powerpc64:

  utgcns/libboost/boost/smart_ptr/detail/sp_counted_impl.hpp:81:5: error:
'get_deleter' declared as a 'virtual' field

This may have something to do with compiler:openmp in USES.  However,
it has broken for more than 6 months at this point.

Approved by:	portmgr (tier-2 blanket)
20 Mar 2020 18:14:24
Original commit files touched by this commit Revision:528792  2.0
jwb search for other commits by this committer
biology/canu: Upgrade to 2.0

Several routine enhancements and bug fixes

Reported by:    portscout
11 Dec 2019 17:53:49
Original commit files touched by this commit Revision:519824  1.9_1
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
08 Nov 2019 14:03:15
Original commit files touched by this commit Revision:517066  1.9
jwb search for other commits by this committer
biology/canu: Upgrade to 1.9

Numerous bug fixes and enhancements

Reported by:    portscout
19 Aug 2019 15:35:28
Original commit files touched by this commit Revision:509290  1.8_5
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 Revision:507372  1.8_4
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
25 Jul 2019 09:02:20
Original commit files touched by this commit Revision:507315  1.8_3
amdmi3 search for other commits by this committer
- Update WWW

Approved by:	portmgr blanket
18 Apr 2019 12:15:56
Original commit files touched by this commit Revision:499251  1.8_3
jwb search for other commits by this committer
biology/canu: Fix build on powerpc64 and aarch64

Should also work on powerpc and arm*, but unable to test

PR:             237105
Reported by:    pkubaj
12 Apr 2019 06:36:31
Original commit files touched by this commit Revision:498698  1.8_3
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
12 Dec 2018 01:35:36
Original commit files touched by this commit Revision:487272  1.8_2
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.

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, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590
12 Dec 2018 00:15:50
Original commit files touched by this commit Revision:487266  1.8_1
jbeich search for other commits by this committer
devel/boost-*: update to 1.69.0

Changes:	http://www.boost.org/users/history/version_1_69_0.html
PR:		232525
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D17645
04 Nov 2018 14:29:03
Original commit files touched by this commit Revision:484077  1.8
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 Revision:476723  1.7_2
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 Revision:475857  1.7_1
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 Revision:473009  1.7
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 Revision:468321  1.7
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 Revision:467711  1.6_3
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 Revision:464084  1.6_2
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 Revision:459315  1.6_1
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 Revision:456982  1.6
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 Revision:456950  1.6
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: 25