BSD Ports

biology/ucsc-userapps 502 FreeBSD

Command line tools from the UCSC Genome Browser project

System
FreeBSD
Repository
FreeBSD ports
Maintainer
[email protected]
Last update
Commit
2414383046
License
MIT
Categories
biology, perl5, python
Package size
10378.1 KiB, 152955.3 KiB installed

Description

These are the command-line bioinformatics utilities associated with the UCSC genome browser. Care has been taken to install only the freely available tools. However, the license information at https://genome.ucsc.edu/license/ is not entirely clear and we may add non-free utilities in the future. Contact UCSC if you are using this port for commercial purposes.

In the other systems

SystemPortVersion
FreeBSDbiology/ucsc-userapps502
HardenedBSDbiology/ucsc-userapps502
GhostBSDbiology/ucsc-userapps502

Install

Binary package:

pkg install ucsc-userapps

From the ports tree:

cd /usr/ports/biology/ucsc-userapps/ && make install clean

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

RUN_DEPENDS=	ucsc-userapps>0:biology/ucsc-userapps

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:latest502502-474-
FreeBSD:14:quarterly502502n/a474-
FreeBSD:15:latest502502n/a474474
FreeBSD:15:quarterly502502n/an/an/a
FreeBSD:16:latest502502n/an/an/a
FreeBSD:16:quarterlyn/an/an/an/an/a

Dependencies

As this port's Makefile names them.

Build 1

Library 4

Runtime 1

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

Build dependencies 33
Run dependencies 32
Required by 1

Configuration

No options to configure.

USES
gmake iconv localbase:ldflags mysql:client shebangfix perl5 python ssl tar:tgz
Service scripts
none

Message after installing

ucsc-kentutils is installed in it's own directory in order to avoid install
conflicts with other ports.  Run "ucsc-shell" to gain access to ucsc-kentutils
commands in your PATH.

This port installs only freely available components of the UCSC userApps
distribution.  See http://genome.ucsc.edu/license/ for more information.

===>   NOTICE:

The ucsc-userapps 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 157
  • bin/kent
  • bin/ucsc-shell
  • userapps/bin/aNotB
  • userapps/bin/addCols
  • userapps/bin/ave
  • userapps/bin/aveCols
  • userapps/bin/bamToPsl
  • userapps/bin/barChartMaxLimit
  • userapps/bin/bedClip
  • userapps/bin/bedCommonRegions
  • userapps/bin/bedGeneParts
  • userapps/bin/bedGraphPack
  • userapps/bin/bedGraphToBigWig
  • userapps/bin/bedJoinTabOffset
  • userapps/bin/bedJoinTabOffset.py
  • userapps/bin/bedPileUps
  • userapps/bin/bedRemoveOverlap
  • userapps/bin/bedRestrictToPositions
  • userapps/bin/bedToBigBed
  • userapps/bin/bigBedInfo
  • userapps/bin/bigBedNamedItems
  • userapps/bin/bigBedSummary
  • userapps/bin/bigBedToBed
  • userapps/bin/bigGuessDb
  • userapps/bin/bigHeat
  • userapps/bin/bigWigAverageOverBed
  • userapps/bin/bigWigCat
  • userapps/bin/bigWigCluster
  • userapps/bin/bigWigCorrelate
  • userapps/bin/bigWigInfo
  • userapps/bin/bigWigMerge
  • userapps/bin/bigWigSummary
  • userapps/bin/bigWigToBedGraph
  • userapps/bin/bigWigToWig
  • userapps/bin/calc
  • userapps/bin/catDir
  • userapps/bin/catUncomment
  • userapps/bin/ccCp
  • userapps/bin/chopFaLines
  • userapps/bin/chromToUcsc
  • userapps/bin/clusterMatrixToBarChartBed
  • userapps/bin/colTransform
  • userapps/bin/convolve
  • userapps/bin/countChars
  • userapps/bin/cpg_lh
  • userapps/bin/detab
  • userapps/bin/dnsInfo
  • userapps/bin/endsInLf
  • userapps/bin/expMatrixToBarchartBed
  • userapps/bin/faAlign
  • userapps/bin/faCmp
  • userapps/bin/faCount
  • userapps/bin/faFilter
  • userapps/bin/faFilterN
  • userapps/bin/faFlyBaseToUcsc
  • userapps/bin/faFrag
  • userapps/bin/faGapLocs
  • userapps/bin/faGapSizes
  • userapps/bin/faNcbiToUcsc
  • userapps/bin/faNoise
  • userapps/bin/faOneRecord
  • userapps/bin/faPolyASizes
  • userapps/bin/faRandomize
  • userapps/bin/faRc
  • userapps/bin/faRenameRecords
  • userapps/bin/faSimplify
  • userapps/bin/faSize
  • userapps/bin/faSomeRecords
  • userapps/bin/faSplit
  • userapps/bin/faToFastq
  • userapps/bin/faToNib
  • userapps/bin/faToTab
  • userapps/bin/faToTwoBit
  • userapps/bin/faTrans
  • userapps/bin/faTrimPolyA
  • userapps/bin/faTrimRead
  • userapps/bin/fastqStatsAndSubsample
  • userapps/bin/fastqToFa
  • userapps/bin/findMotif
  • userapps/bin/fixCr
  • userapps/bin/gapSplit
  • userapps/bin/gffPeek
  • userapps/bin/git-reports
  • userapps/bin/gmtime
  • userapps/bin/headRest
  • userapps/bin/htmlCheck
  • userapps/bin/htmlPics
  • userapps/bin/hubtools
  • userapps/bin/jkUniq
  • userapps/bin/lineCount
  • userapps/bin/linesToRa
  • userapps/bin/localtime
  • userapps/bin/matrixClusterColumns
  • userapps/bin/matrixMarketToTsv
  • userapps/bin/matrixNormalize
  • userapps/bin/matrixToBarChartBed
  • userapps/bin/mktime
  • userapps/bin/newProg
  • userapps/bin/newPythonProg
  • userapps/bin/nibFrag

The first 100 are listed.

distinfo 1
FileSizeSHA256
userApps.v502.src.tgz2.9944124e+0738e29dbf7c1e6d49aaf358014960c5781fd59aa3b7b406dadc9557c98e895f22
Master sites 1
  • https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/

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.
7b5805c0b6 Jason W. Bacon biology/ucsc-userapps: Update to v502
Many fixes and enhancements since v474 Changes: https://github.com/ucscGenomeBrowser/kent/releases Reported by: portscout