FreeBSD Ports

biology/bbmap 40.02

BBMap short read aligner, and other bioinformatic tools

Repository
FreeBSD ports
Maintainer
[email protected]
Last update
Commit
2414383046
License
BSD3CLAUSE
Categories
biology, java
Package size
9912.1 KiB, 44041.7 KiB installed

Description

This package includes BBMap, a short read aligner, as well as various other bioinformatic tools. It is written in pure Java, can run on any platform, and has no dependencies other than Java being installed (compiled for Java 6 and higher). All tools are efficient and multithreaded.

Install

As a binary package — by origin, or by package name:

pkg install biology/bbmap
pkg install bbmap

From the ports tree:

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

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

RUN_DEPENDS=	bbmap>0:biology/bbmap

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:latest40.0240.0238.9239.3440.02
FreeBSD:14:quarterly40.0240.02n/a39.1540.02
FreeBSD:15:latest40.0240.02n/a--
FreeBSD:15:quarterly40.0240.02n/an/an/a
FreeBSD:16:latest40.0240.02n/an/an/a
FreeBSD:16:quarterlyn/an/an/an/an/a

Dependencies

As this port's Makefile names them.

Runtime 3

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

All run dependencies 57
Required by 1

Configuration

No options to configure.

USES
java shebangfix
Service scripts
none

Message after installing

===>   NOTICE:

The bbmap 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 3866
  • bin/bbduk.sh
  • bin/bbmap.sh
  • bin/bbmerge.sh
  • bin/bbnorm.sh
  • bin/bbsplit.sh
  • bin/bbversion.sh
  • bin/bloomfilter.sh
  • bin/callvariants.sh
  • bin/clumpify.sh
  • bin/comparesketch.sh
  • bin/dedupe.sh
  • bin/reformat.sh
  • bin/sendsketch.sh
  • bin/tadpole.sh
  • libexec/bbmap/a_sample_mt.sh
  • libexec/bbmap/addadapters.sh
  • libexec/bbmap/addssu.sh
  • libexec/bbmap/addx.sh
  • libexec/bbmap/adjusthomopolymers.sh
  • libexec/bbmap/alignerbenchmark.sh
  • libexec/bbmap/alignrandom.sh
  • libexec/bbmap/alltoall.sh
  • libexec/bbmap/analyzeaccession.sh
  • libexec/bbmap/analyzegenes.sh
  • libexec/bbmap/analyzesketchresults.sh
  • libexec/bbmap/applyvariants.sh
  • libexec/bbmap/balancevectors.sh
  • libexec/bbmap/bamlinestreamer.sh
  • libexec/bbmap/bandedaligner.sh
  • libexec/bbmap/bandedplusaligner.sh
  • libexec/bbmap/bbcms.sh
  • libexec/bbmap/bbcountunique.sh
  • libexec/bbmap/bbcrisprfinder.sh
  • libexec/bbmap/bbduk.sh
  • libexec/bbmap/bbdukOld.sh
  • libexec/bbmap/bbdukS.sh
  • libexec/bbmap/bbest.sh
  • libexec/bbmap/bbfakereads.sh
  • libexec/bbmap/bbmap.sh
  • libexec/bbmap/bbmap5.sh
  • libexec/bbmap/bbmapacc.sh
  • libexec/bbmap/bbmapskimmer.sh
  • libexec/bbmap/bbmask.sh
  • libexec/bbmap/bbmerge-auto.sh
  • libexec/bbmap/bbmerge.sh
  • libexec/bbmap/bbnorm.sh
  • libexec/bbmap/bbrealign.sh
  • libexec/bbmap/bbrename.sh
  • libexec/bbmap/bbsketch.sh
  • libexec/bbmap/bbsort.sh
  • libexec/bbmap/bbsplit.sh
  • libexec/bbmap/bbsplitpairs.sh
  • libexec/bbmap/bbstats.sh
  • libexec/bbmap/bbversion.sh
  • libexec/bbmap/bbwrap.sh
  • libexec/bbmap/bedset.sh
  • libexec/bbmap/bloomfilter.sh
  • libexec/bbmap/bloomfilterparser.sh
  • libexec/bbmap/calcmem.sh
  • libexec/bbmap/calctruequality.sh
  • libexec/bbmap/calibrate.sh
  • libexec/bbmap/callgenes.sh
  • libexec/bbmap/callpeaks.sh
  • libexec/bbmap/callvariants.sh
  • libexec/bbmap/callvariants2.sh
  • libexec/bbmap/cat.sh
  • libexec/bbmap/cbcl2text.sh
  • libexec/bbmap/cg2illumina.sh
  • libexec/bbmap/checkstrand.sh
  • libexec/bbmap/cladeloader.sh
  • libexec/bbmap/cladeserver.sh
  • libexec/bbmap/cloudplot.sh
  • libexec/bbmap/clumpify.sh
  • libexec/bbmap/commonkmers.sh
  • libexec/bbmap/comparegff.sh
  • libexec/bbmap/comparelabels.sh
  • libexec/bbmap/comparesketch.sh
  • libexec/bbmap/comparessu.sh
  • libexec/bbmap/comparevcf.sh
  • libexec/bbmap/consect.sh
  • libexec/bbmap/consensus.sh
  • libexec/bbmap/copyfile.sh
  • libexec/bbmap/countbarcodes.sh
  • libexec/bbmap/countbarcodes2.sh
  • libexec/bbmap/countduplicates.sh
  • libexec/bbmap/countgc.sh
  • libexec/bbmap/countsharedlines.sh
  • libexec/bbmap/covmaker.sh
  • libexec/bbmap/crossblock.sh
  • libexec/bbmap/crosscontaminate.sh
  • libexec/bbmap/crosscutaligner.sh
  • libexec/bbmap/cutgff.sh
  • libexec/bbmap/cutprimers.sh
  • libexec/bbmap/ddlblacklist.sh
  • libexec/bbmap/ddlcalibrate.sh
  • libexec/bbmap/ddlcompare.sh
  • libexec/bbmap/ddlmerger.sh
  • libexec/bbmap/ddlwriter.sh
  • libexec/bbmap/decontaminate.sh
  • libexec/bbmap/dedupe.sh

The first 100 are listed.

distinfo 1
FileSizeSHA256
bbushnell-BBTools-v40.02_GH0.tar.gz3.0250324e+074faec10a452ea7974c778c3c207a7885e43e639a89b9a360b6d16bfb9b61a6cd

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.
148f5ec1fb Jason W. Bacon biology/bbmap: Update to 40.02
Many fixes and improvements since v39.34 Changes: https://github.com/bbushnell/BBTools/commits/master/ Reported by: portscout