notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)
Ukraine
Some details on the 2023-01-16 website outage.
We just rebooted with several updates: * new HMTLify code * no port maintainer is now highly visible (e.g. https://freshports.org/security/sssd/) * fixed search logic error when using plain/ text details at https://github.com/FreshPorts/freshports/releases/tag/2.2.34
Port details
canu Single molecule sequence assembler
2.2_2 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 Version 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: 2022-09-07 21:58:51
Commit Hash: fb16dfe
Also Listed In: java perl5
License: GPLv2
Description:
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb
pkg-plist: as obtained via: make generate-plist
Expand this list (84 items)
Collapse this list.
  1. /usr/local/share/licenses/canu-2.2_2/catalog.mk
  2. /usr/local/share/licenses/canu-2.2_2/LICENSE
  3. /usr/local/share/licenses/canu-2.2_2/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
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
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:

Packages (timestamps in pop-ups are UTC):
canu
ABIlatestquarterly
FreeBSD:11:aarch64pkg-falloutpkg-fallout
FreeBSD:11:amd642.1_12.1_1
FreeBSD:11:armv6pkg-falloutpkg-fallout
FreeBSD:11:i386pkg-falloutpkg-fallout
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips64pkg-falloutpkg-fallout
FreeBSD:12:aarch64pkg-fallout2.2_2
FreeBSD:12:amd642.2_22.2_2
FreeBSD:12:armv6pkg-falloutpkg-fallout
FreeBSD:12:armv7pkg-falloutpkg-fallout
FreeBSD:12:i386pkg-falloutpkg-fallout
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips64pkg-falloutpkg-fallout
FreeBSD:12:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:aarch642.2_22.2_2
FreeBSD:13:amd642.2_22.2_2
FreeBSD:13:armv6pkg-falloutpkg-fallout
FreeBSD:13:armv7pkg-falloutpkg-fallout
FreeBSD:13:i386pkg-falloutpkg-fallout
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips64pkg-falloutpkg-fallout
FreeBSD:13:powerpc64pkg-fallout2.2_2
FreeBSD:13:riscv64pkg-falloutpkg-fallout
FreeBSD:14:aarch642.2_2pkg-fallout
FreeBSD:14:amd642.2_2pkg-fallout
FreeBSD:14:armv6pkg-falloutpkg-fallout
FreeBSD:14:armv7pkg-falloutpkg-fallout
FreeBSD:14:i386pkg-falloutpkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips64pkg-falloutpkg-fallout
FreeBSD:14:powerpc642.2_2pkg-fallout
FreeBSD:14:riscv64pkg-falloutpkg-fallout
 

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/v2.2/
Collapse this list.

Number of commits found: 31

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
07 Sep 2022 21:58:51
commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
2.2_2
07 Sep 2022 21:10:59
commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
2.2_2
12 Aug 2022 14:46:53
commit hash:4cf39decb348615b9c8a28370d987a85d1b8a5edcommit hash:4cf39decb348615b9c8a28370d987a85d1b8a5edcommit hash:4cf39decb348615b9c8a28370d987a85d1b8a5edcommit hash:4cf39decb348615b9c8a28370d987a85d1b8a5ed files touched by this commit
Dima Panov (fluffy) search for other commits by this committer
*/*: bump all consumers after recent boost upgrade
2.2_1
22 May 2022 20:17:16
commit hash:b082b3d13e8c4872b73fb681eb99b261926ac9cdcommit hash:b082b3d13e8c4872b73fb681eb99b261926ac9cdcommit hash:b082b3d13e8c4872b73fb681eb99b261926ac9cdcommit hash:b082b3d13e8c4872b73fb681eb99b261926ac9cd files touched by this commit
Dima Panov (fluffy) search for other commits by this committer
devel/boost-all: bump all library consumers after boost upgrade

PR:	246106
2.2
20 Dec 2021 12:59:13
commit hash:b2dab386316742576c3fc3fd7a3ed0284c919683commit hash:b2dab386316742576c3fc3fd7a3ed0284c919683commit hash:b2dab386316742576c3fc3fd7a3ed0284c919683commit hash:b2dab386316742576c3fc3fd7a3ed0284c919683 files touched by this commit
Antoine Brodin (antoine) search for other commits by this committer
biology/canu: fix CATEGORIES
2.2
19 Dec 2021 21:06:56
commit hash:b9105b7ef1e91bce177273f3031a98781ca6faf7commit hash:b9105b7ef1e91bce177273f3031a98781ca6faf7commit hash:b9105b7ef1e91bce177273f3031a98781ca6faf7commit hash:b9105b7ef1e91bce177273f3031a98781ca6faf7 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/canu: Update to 2.2

FreeBSD port: Add support for aarch64 and powerpc64 using simde
Not yet supported upstream

Several upstream bug fixes and minor enhancements since 2.1

Changes: https://github.com/marbl/canu/tags
2.1_1
07 Apr 2021 08:09:01
commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
2.1_1
06 Apr 2021 14:31:07
commit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
2.1_1
11 Jan 2021 16:51:16
Revision:561227Original commit files touched by this commit
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
2.1
14 Sep 2020 22:27:37
Revision:548685Original commit files touched by this commit
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
2.0
17 May 2020 02:25:17
Revision:535507Original commit files touched by this commit
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)
2.0
20 Mar 2020 18:14:24
Revision:528792Original commit files touched by this commit
jwb search for other commits by this committer
biology/canu: Upgrade to 2.0

Several routine enhancements and bug fixes

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

Numerous bug fixes and enhancements

Reported by:    portscout
1.8_5
19 Aug 2019 15:35:28
Revision:509290Original commit files touched by this commit
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
1.8_4
26 Jul 2019 20:46:57
Revision:507372Original commit files touched by this commit
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
1.8_3
25 Jul 2019 09:02:20
Revision:507315Original commit files touched by this commit
amdmi3 search for other commits by this committer
- Update WWW

Approved by:	portmgr blanket
1.8_3
18 Apr 2019 12:15:56
Revision:499251Original commit files touched by this commit
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
1.8_3
12 Apr 2019 06:36:31
Revision:498698Original commit files touched by this commit
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
1.8_2
12 Dec 2018 01:35:36
Revision:487272Original commit files touched by this commit
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
1.8_1
12 Dec 2018 00:15:50
Revision:487266Original commit files touched by this commit
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
1.8
04 Nov 2018 14:29:03
Revision:484077Original commit files touched by this commit
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)
1.7_2
09 Aug 2018 06:58:31
Revision:476723Original commit files touched by this commit
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
1.7_1
29 Jul 2018 22:18:46
Revision:475857Original commit files touched by this commit
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
1.7
21 Jun 2018 23:52:37
Revision:473009Original commit files touched by this commit
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)
1.7
26 Apr 2018 04:16:15
Revision:468321Original commit files touched by this commit
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
1.6_3
18 Apr 2018 13:57:43
Revision:467711Original commit files touched by this commit
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
1.6_2
10 Mar 2018 17:46:06
Revision:464084Original commit files touched by this commit
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).
1.6_1
18 Jan 2018 04:11:03
Revision:459315Original commit files touched by this commit
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
1.6
22 Dec 2017 14:14:11
Revision:456982Original commit files touched by this commit
jwb search for other commits by this committer
biology/canu: Replace += with = for depends

Approved by:    jrm
Differential Revision:  https://reviews.freebsd.org/D13574
1.6
22 Dec 2017 01:30:27
Revision:456950Original commit files touched by this commit
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: 31