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Port details
canu Single molecule sequence assembler
1.8_5 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 1.8Version 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: 2019-08-19 16:35:28
SVN Revision: 509290
Also Listed In: java perl5
License: GPLv2
Description:
SVNWeb : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (84 items)
  1. /usr/local/share/licenses/canu-1.8_5/catalog.mk
  2. /usr/local/share/licenses/canu-1.8_5/LICENSE
  3. /usr/local/share/licenses/canu-1.8_5/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
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: pkg install canu
PKGNAME: canu
Flavors: there is no flavor information for this port.
distinfo:

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake : devel/gmake
  2. gcc9 : lang/gcc9
  3. as : devel/binutils
  4. perl5>=5.30.r1<5.31 : lang/perl5.30
Runtime dependencies:
  1. gnuplot : math/gnuplot
  2. java : java/openjdk8
  3. gcc9 : lang/gcc9
  4. perl5>=5.30.r1<5.31 : lang/perl5.30
Library dependencies:
  1. libboost_regex.so : devel/boost-libs
There are no ports dependent upon this port

Configuration Options

USES:

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

Number of commits found: 17

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
19 Aug 2019 15:35:28
Original commit files touched by this commit  1.8_5
Revision:509290
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  1.8_4
Revision:507372
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  1.8_3
Revision:507315
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  1.8_3
Revision:499251
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  1.8_3
Revision:498698
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  1.8_2
Revision:487272
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  1.8_1
Revision:487266
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  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: 17

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