BSD Ports

biology/canu 2.3 FreeBSD

Single molecule sequence assembler

System
FreeBSD
Repository
FreeBSD ports
Maintainer
[email protected]
Last update
Commit
2414383046
License
GPLv2
Categories
biology, java, perl5
Package size
3813.3 KiB, 29445.2 KiB installed

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

In the other systems

SystemPortVersion
FreeBSDbiology/canu2.3
NetBSDbiology/canu2.2nb11
DragonFlybiology/canu2.2_6
HardenedBSDbiology/canu2.3
GhostBSDbiology/canu2.3

Install

Binary package:

pkg install canu

From the ports tree:

cd /usr/ports/biology/canu/ && make install clean

To depend on this port in another port's Makefile:

RUN_DEPENDS=	canu>0:biology/canu

Packages

The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.

Repositoryaarch64amd64armv6armv7i386
FreeBSD:14:latest2.32.3---
FreeBSD:14:quarterly2.32.3n/a--
FreeBSD:15:latest2.32.3n/a--
FreeBSD:15:quarterly2.32.3n/an/an/a
FreeBSD:16:latest2.32.3n/an/an/a
FreeBSD:16:quarterlyn/an/an/an/an/a

Dependencies

As this port's Makefile names them.

Build 1

Library 1

Runtime 1

The full lists below include those, and their dependencies in turn.

Build dependencies 16
Run dependencies 136

The first 100 are listed.

No port depends on this one.

Configuration

No options to configure.

USES
compiler:c++11-lang gmake java:run localbase perl5 pkgconfig ssl tar:xz
Service scripts
none

Message after installing

===>   NOTICE:

The canu port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:

https://bugs.freebsd.org/bugzilla

More information about port maintainership is available at:

https://docs.freebsd.org/en/articles/contributing/#ports-contributing

Files

pkg-plist 78
  • bin/alignGFA
  • bin/bogart
  • bin/canu
  • bin/canu-time
  • bin/canu.defaults
  • bin/correctOverlaps
  • bin/draw-tig
  • bin/dumpBlob
  • bin/edalign
  • bin/errorEstimate
  • bin/falconsense
  • bin/filterCorrectionLayouts
  • bin/filterCorrectionOverlaps
  • bin/findErrors
  • bin/findErrors-Dump
  • bin/fixErrors
  • bin/generateCorrectionLayouts
  • bin/layoutReads
  • bin/layoutToPackage
  • bin/loadCorrectedReads
  • bin/loadErates
  • bin/loadTrimmedReads
  • bin/mergeRanges
  • bin/meryl
  • bin/mhapConvert
  • bin/mmapConvert
  • bin/ovStoreBucketizer
  • bin/ovStoreBuild
  • bin/ovStoreConfig
  • bin/ovStoreDump
  • bin/ovStoreIndexer
  • bin/ovStoreSorter
  • bin/ovStoreStats
  • bin/overlapAlign
  • bin/overlapConvert
  • bin/overlapImport
  • bin/overlapInCore
  • bin/overlapInCorePartition
  • bin/overlapPair
  • bin/seqrequester
  • bin/splitHaplotype
  • bin/splitReads
  • bin/sqStoreCreate
  • bin/sqStoreDumpFASTQ
  • bin/sqStoreDumpMetaData
  • bin/tgStoreCompress
  • bin/tgStoreDump
  • bin/tgStoreLoad
  • bin/tgTigDisplay
  • bin/trimReads
  • bin/utgcns
  • lib/libcanu.a
  • %%SITE_PERL%%/canu/Configure.pm
  • %%SITE_PERL%%/canu/Consensus.pm
  • %%SITE_PERL%%/canu/CorrectReads.pm
  • %%SITE_PERL%%/canu/Defaults.pm
  • %%SITE_PERL%%/canu/Execution.pm
  • %%SITE_PERL%%/canu/Grid.pm
  • %%SITE_PERL%%/canu/Grid_Cloud.pm
  • %%SITE_PERL%%/canu/Grid_DNANexus.pm
  • %%SITE_PERL%%/canu/Grid_LSF.pm
  • %%SITE_PERL%%/canu/Grid_Local.pm
  • %%SITE_PERL%%/canu/Grid_PBSTorque.pm
  • %%SITE_PERL%%/canu/Grid_SGE.pm
  • %%SITE_PERL%%/canu/Grid_Slurm.pm
  • %%SITE_PERL%%/canu/HaplotypeReads.pm
  • %%SITE_PERL%%/canu/Meryl.pm
  • %%SITE_PERL%%/canu/Output.pm
  • %%SITE_PERL%%/canu/OverlapBasedTrimming.pm
  • %%SITE_PERL%%/canu/OverlapErrorAdjustment.pm
  • %%SITE_PERL%%/canu/OverlapInCore.pm
  • %%SITE_PERL%%/canu/OverlapMMap.pm
  • %%SITE_PERL%%/canu/OverlapMhap.pm
  • %%SITE_PERL%%/canu/OverlapStore.pm
  • %%SITE_PERL%%/canu/Report.pm
  • %%SITE_PERL%%/canu/SequenceStore.pm
  • %%SITE_PERL%%/canu/Unitig.pm
  • %%JAVAJARDIR%%/mhap-2.1.3.jar
distinfo 1
FileSizeSHA256
canu-2.3.tar.xz3.065692e+06ecb071943cde722152deb861d4ab897090f00b227fd0b261592e1e3fdd3e3e1a
Master sites 1
  • https://github.com/marbl/canu/releases/download/v2.3/

Commit history 2

DateCommitCreditsLog message
2414383046 Jason W. Bacon Release numerous ports to ports@
I've been retired for a few years, and it is unlikely I will be doing any more scientific computing support in the future. I have continued to maintain ~160 ports to the best of my ability, mainly as a favor to the community, but I can no longer justify the time and effort required. I am therefore releasing most of my scientific ports, along with a few others, to ports@. I will continue to maintain ports I am actively using and those for which I am upstream.
169b5109c4 Jason W. Bacon biology/canu: Update to 2.3
Several bug fixes and enhancements Changes: https://github.com/marbl/canu/releases Should fix package build on arm64 Change WWW to something portscout can use Reported by: pkg-fallout