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Port details
ucsc-userapps Command line tools from the UCSC Genome Browser project
474 biology on this many watch lists=2 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 414_1Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-04-25 17:21:12
Last Update: 2024-11-28 15:59:20
Commit Hash: 9cb153a
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
Also Listed In: perl5 python
License: MIT
WWW:
https://hgdownload.cse.ucsc.edu/admin/exe/
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.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb - no subversion history for this port

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (161 items)
Collapse this list.
  1. /usr/local/share/licenses/ucsc-userapps-474/catalog.mk
  2. /usr/local/share/licenses/ucsc-userapps-474/LICENSE
  3. /usr/local/share/licenses/ucsc-userapps-474/MIT
  4. bin/kent
  5. bin/ucsc-shell
  6. userapps/bin/aNotB
  7. userapps/bin/addCols
  8. userapps/bin/ave
  9. userapps/bin/aveCols
  10. userapps/bin/bamToPsl
  11. userapps/bin/barChartMaxLimit
  12. userapps/bin/bedClip
  13. userapps/bin/bedCommonRegions
  14. userapps/bin/bedGeneParts
  15. userapps/bin/bedGraphPack
  16. userapps/bin/bedGraphToBigWig
  17. userapps/bin/bedJoinTabOffset
  18. userapps/bin/bedJoinTabOffset.py
  19. userapps/bin/bedPileUps
  20. userapps/bin/bedRemoveOverlap
  21. userapps/bin/bedRestrictToPositions
  22. userapps/bin/bedToBigBed
  23. userapps/bin/bigBedInfo
  24. userapps/bin/bigBedNamedItems
  25. userapps/bin/bigBedSummary
  26. userapps/bin/bigBedToBed
  27. userapps/bin/bigGuessDb
  28. userapps/bin/bigHeat
  29. userapps/bin/bigWigAverageOverBed
  30. userapps/bin/bigWigCat
  31. userapps/bin/bigWigCluster
  32. userapps/bin/bigWigCorrelate
  33. userapps/bin/bigWigInfo
  34. userapps/bin/bigWigMerge
  35. userapps/bin/bigWigSummary
  36. userapps/bin/bigWigToBedGraph
  37. userapps/bin/bigWigToWig
  38. userapps/bin/calc
  39. userapps/bin/catDir
  40. userapps/bin/catUncomment
  41. userapps/bin/ccCp
  42. userapps/bin/chopFaLines
  43. userapps/bin/chromToUcsc
  44. userapps/bin/clusterMatrixToBarChartBed
  45. userapps/bin/colTransform
  46. userapps/bin/convolve
  47. userapps/bin/countChars
  48. userapps/bin/cpg_lh
  49. userapps/bin/detab
  50. userapps/bin/dnsInfo
  51. userapps/bin/endsInLf
  52. userapps/bin/expMatrixToBarchartBed
  53. userapps/bin/faAlign
  54. userapps/bin/faCmp
  55. userapps/bin/faCount
  56. userapps/bin/faFilter
  57. userapps/bin/faFilterN
  58. userapps/bin/faFlyBaseToUcsc
  59. userapps/bin/faFrag
  60. userapps/bin/faGapLocs
  61. userapps/bin/faGapSizes
  62. userapps/bin/faNcbiToUcsc
  63. userapps/bin/faNoise
  64. userapps/bin/faOneRecord
  65. userapps/bin/faPolyASizes
  66. userapps/bin/faRandomize
  67. userapps/bin/faRc
  68. userapps/bin/faRenameRecords
  69. userapps/bin/faSimplify
  70. userapps/bin/faSize
  71. userapps/bin/faSomeRecords
  72. userapps/bin/faSplit
  73. userapps/bin/faToFastq
  74. userapps/bin/faToNib
  75. userapps/bin/faToTab
  76. userapps/bin/faToTwoBit
  77. userapps/bin/faTrans
  78. userapps/bin/faTrimPolyA
  79. userapps/bin/faTrimRead
  80. userapps/bin/fastqStatsAndSubsample
  81. userapps/bin/fastqToFa
  82. userapps/bin/findMotif
  83. userapps/bin/fixCr
  84. userapps/bin/gapSplit
  85. userapps/bin/gffPeek
  86. userapps/bin/git-reports
  87. userapps/bin/gmtime
  88. userapps/bin/headRest
  89. userapps/bin/htmlCheck
  90. userapps/bin/htmlPics
  91. userapps/bin/jkUniq
  92. userapps/bin/lineCount
  93. userapps/bin/linesToRa
  94. userapps/bin/localtime
  95. userapps/bin/matrixClusterColumns
  96. userapps/bin/matrixMarketToTsv
  97. userapps/bin/matrixNormalize
  98. userapps/bin/matrixToBarChartBed
  99. userapps/bin/mktime
  100. userapps/bin/newProg
  101. userapps/bin/newPythonProg
  102. userapps/bin/nibFrag
  103. userapps/bin/nibSize
  104. userapps/bin/nt4Frag
  105. userapps/bin/paraFetch
  106. userapps/bin/paraSync
  107. userapps/bin/pslMap
  108. userapps/bin/pslMapPostChain
  109. userapps/bin/pslPosTarget
  110. userapps/bin/pslProtToRnaCoords
  111. userapps/bin/pslRc
  112. userapps/bin/pslRemoveFrameShifts
  113. userapps/bin/pslScore
  114. userapps/bin/pslSpliceJunctions
  115. userapps/bin/pslSwap
  116. userapps/bin/pslToPslx
  117. userapps/bin/pslToXa
  118. userapps/bin/raToLines
  119. userapps/bin/raToTab
  120. userapps/bin/randomLines
  121. userapps/bin/rmFaDups
  122. userapps/bin/rowsToCols
  123. userapps/bin/scrambleFa
  124. userapps/bin/sizeof
  125. userapps/bin/spacedToTab
  126. userapps/bin/splitFile
  127. userapps/bin/splitFileByColumn
  128. userapps/bin/strexCalc
  129. userapps/bin/stringify
  130. userapps/bin/subChar
  131. userapps/bin/subColumn
  132. userapps/bin/subs
  133. userapps/bin/tabToMmHash
  134. userapps/bin/tableSum
  135. userapps/bin/tailLines
  136. userapps/bin/tdbRename
  137. userapps/bin/tdbSort
  138. userapps/bin/textHist2
  139. userapps/bin/textHistogram
  140. userapps/bin/tickToDate
  141. userapps/bin/toLower
  142. userapps/bin/toUpper
  143. userapps/bin/trackDbIndexBb
  144. userapps/bin/twoBitDup
  145. userapps/bin/twoBitInfo
  146. userapps/bin/twoBitToFa
  147. userapps/bin/ucscApiClient
  148. userapps/bin/udcCleanup
  149. userapps/bin/undupFa
  150. userapps/bin/upper
  151. userapps/bin/vcfFilter
  152. userapps/bin/venn
  153. userapps/bin/verticalSplitSqlTable
  154. userapps/bin/webSync
  155. userapps/bin/weedLines
  156. userapps/bin/wigCorrelate
  157. userapps/bin/wigToBigWig
  158. userapps/bin/wordLine
  159. @owner
  160. @group
  161. @mode
Collapse this list.
Dependency lines:
  • ucsc-userapps>0:biology/ucsc-userapps
To install the port:
cd /usr/ports/biology/ucsc-userapps/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/ucsc-userapps
  • pkg install ucsc-userapps
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: ucsc-userapps
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1732796640 SHA256 (userApps.v474.src.tgz) = 87c465169b1246c3d2f56ea415461b7b2a4fb24bf5b7b95a3b590274cc7daec7 SIZE (userApps.v474.src.tgz) = 24402279

Packages (timestamps in pop-ups are UTC):
ucsc-userapps
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest472474--474---
FreeBSD:13:quarterly--------
FreeBSD:14:latest-474--474---
FreeBSD:14:quarterly--------
FreeBSD:15:latest472472n/a472n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. bash : shells/bash
  2. gmake>=4.4.1 : devel/gmake
  3. python3.11 : lang/python311
  4. perl5>=5.36<5.37 : lang/perl5.36
Test dependencies:
  1. python3.11 : lang/python311
Runtime dependencies:
  1. bash : shells/bash
  2. python3.11 : lang/python311
  3. perl5>=5.36<5.37 : lang/perl5.36
Library dependencies:
  1. libmysqlclient.so : databases/mysql80-client
  2. libunwind.so : devel/libunwind
  3. libfreetype.so : print/freetype2
  4. libpng.so : graphics/png
This port is required by:
for Run
  1. biology/biostar-tools

Configuration Options:
No options to configure
Options name:
biology_ucsc-userapps
USES:
gmake iconv localbase:ldflags shebangfix perl5 python:3.6+ ssl tar:tgz
pkg-message:
For install:
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.
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/
Collapse this list.

Number of commits found: 14

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
474
28 Nov 2024 15:59:20
commit hash: 9cb153ab34840d98a13cde17c524498a70cdd7f3commit hash: 9cb153ab34840d98a13cde17c524498a70cdd7f3commit hash: 9cb153ab34840d98a13cde17c524498a70cdd7f3commit hash: 9cb153ab34840d98a13cde17c524498a70cdd7f3 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/ucsc-userapps: Update to v474

Several fixes and a few enhancements since v472
Changes: https://github.com/ucscGenomeBrowser/kent/releases

Reported by:    portscout
472
14 Nov 2024 08:41:02
commit hash: 4bbe42aa51c5c715520dc21d871a452235079999commit hash: 4bbe42aa51c5c715520dc21d871a452235079999commit hash: 4bbe42aa51c5c715520dc21d871a452235079999commit hash: 4bbe42aa51c5c715520dc21d871a452235079999 files touched by this commit
Robert Clausecker (fuz) search for other commits by this committer
biology/ucsc-userapps: remove ONLY_FOR_ARCHS

Builds fine on arm64, armv7, and i386.  Seems like the x86-only
function is no longer required.

Approved by:	portmgr (build fix blanket)
472
07 Nov 2024 23:41:53
commit hash: 04d8b3b43354d64c5a6040e2bc61bbd0c8968ef0commit hash: 04d8b3b43354d64c5a6040e2bc61bbd0c8968ef0commit hash: 04d8b3b43354d64c5a6040e2bc61bbd0c8968ef0commit hash: 04d8b3b43354d64c5a6040e2bc61bbd0c8968ef0 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/ucsc-userapps: Change license to MIT

Old license did not allow packaging
This port still excludes a few tools that are non-free
472
07 Nov 2024 13:17:36
commit hash: aaa110d4b8fe64383826e03507d1cd4753a607edcommit hash: aaa110d4b8fe64383826e03507d1cd4753a607edcommit hash: aaa110d4b8fe64383826e03507d1cd4753a607edcommit hash: aaa110d4b8fe64383826e03507d1cd4753a607ed files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/ucsc-userapps: Update to 472

Numerous fixes and enhancements since v414
Changes: https://github.com/ucscGenomeBrowser/kent/releases

Reported by:    fuz
414_1
30 Dec 2023 07:16:41
commit hash: 9ee2e860d43ba37a60bb66a3b7189e9403a393b9commit hash: 9ee2e860d43ba37a60bb66a3b7189e9403a393b9commit hash: 9ee2e860d43ba37a60bb66a3b7189e9403a393b9commit hash: 9ee2e860d43ba37a60bb66a3b7189e9403a393b9 files touched by this commit
Muhammad Moinur Rahman (bofh) search for other commits by this committer
biology/ucsc-userapps: Replace dependencies

Currently their is a hardcoded dependency on mysql57-client which is
about to be removed. Ports depending on mysql should always use
USES=mysql rather than hardcoded *_DEPENDS. As I do not have a licensed
version of this application for now switch to USES=mysql. This should
not affect the cluster build at all as this is a RESTRICTED ports.

Approved by:	portmgr (blanket)
414_1
27 Jun 2023 19:34:34
commit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacbcommit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacbcommit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacbcommit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacb files touched by this commit
Rene Ladan (rene) search for other commits by this committer
all: remove explicit versions in USES=python for "3.x+"

The logic in USES=python will automatically convert this to 3.8+ by
itself.

Adjust two ports that only had Python 3.7 mentioned but build fine
on Python 3.8 too.

finance/quickfix: mark BROKEN with PYTHON

libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I../.. -I -I. -I.. -I../.. -I../C++
-DLIBICONV_PLUG -DPYTHON_MAJOR_VERSION=3 -Wno-unused-variable
-Wno-maybe-uninitialized -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong
-fno-strict-aliasing -DLIBICONV_PLUG -Wall -ansi
-Wno-unused-command-line-argument -Wpointer-arith -Wwrite-strings
-Wno-overloaded-virtual -Wno-deprecated-declarations -Wno-deprecated -std=c++0x
-MT _quickfix_la-QuickfixPython.lo -MD -MP -MF
.deps/_quickfix_la-QuickfixPython.Tpo -c QuickfixPython.cpp  -fPIC -DPIC -o
.libs/_quickfix_la-QuickfixPython.o
warning: unknown warning option '-Wno-maybe-uninitialized'; did you mean
'-Wno-uninitialized'? [-Wunknown-warning-option]
QuickfixPython.cpp:175:11: fatal error: 'Python.h' file not found
          ^~~~~~~~~~
1 warning and 1 error generated.

Reviewed by:	portmgr, vishwin, yuri
Differential Revision:	<https://reviews.freebsd.org/D40568>
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)
414_1
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)
414_1
20 Jul 2022 14:20:57
commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 files touched by this commit
Tobias C. Berner (tcberner) search for other commits by this committer
biology: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Akinori MUSHA aka knu <knu@idaemons.org>
  *  Andrey Zakhvatov
  *  Bob Zimmermann <rpz@cse.wustl.edu>
  *  Camson Huynh <chuynh@biolateral.com.au>
  *  Dan Siercks <dsiercks@uwm.edu>
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Hannes Hauswedell <h2+fbsdports@fsfe.org>
  *  J. Bacon <jwb@FreeBSD.org>
  *  Jason Bacon <jwb@FreeBSD.org>
  *  Jeremy <karlj000@unbc.ca>
(Only the first 15 lines of the commit message are shown above View all of this commit message)
414_1
25 Oct 2021 12:58:29
commit hash: 61b661339366b6ee95ca1de0667979da9240c6b8commit hash: 61b661339366b6ee95ca1de0667979da9240c6b8commit hash: 61b661339366b6ee95ca1de0667979da9240c6b8commit hash: 61b661339366b6ee95ca1de0667979da9240c6b8 files touched by this commit
Alexey Dokuchaev (danfe) search for other commits by this committer
Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)

ONLY_FOR_ARCHS_REASON is used as part of the sentence and thus should
start with lower-case letter and not end with a period which is added
by the framework, similar to other knobs like BROKEN, IGNORE, et al.

While here, remove needless quoting, add missing Oxford comma, expand
contractions and jargonisms, use correct spelling for proper names.
414_1
24 Sep 2021 21:53:30
commit hash: d94f19ab9ffcd2fac7650802d6aea3f68156f5d7commit hash: d94f19ab9ffcd2fac7650802d6aea3f68156f5d7commit hash: d94f19ab9ffcd2fac7650802d6aea3f68156f5d7commit hash: d94f19ab9ffcd2fac7650802d6aea3f68156f5d7 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/ucsc-userapps: Add "kent" command in ${PREFIX}/bin

Standard kent userapps commands are installed under ${PREFIX}/userapps
because of multiple conflicts.  The kent command turns the standard
commands into subcommands, so no special PATH is needed.

    /usr/local/ucsc-userapps/bin/bigWigToBedGraph [args]

can be run as

    kent bigWigToBedGraph [args]
414
15 May 2021 15:23:08
commit hash: 43397d188c684b83c4bff3e9b78862a1f6ab47f7commit hash: 43397d188c684b83c4bff3e9b78862a1f6ab47f7commit hash: 43397d188c684b83c4bff3e9b78862a1f6ab47f7commit hash: 43397d188c684b83c4bff3e9b78862a1f6ab47f7 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/ucsc-userapps: Update to v414

Update license message.  Confirmed via conversation with UCSC that some
proprietary code is used in the "free" tools build.  UCSC is working on it.
413
06 May 2021 11:47:41
commit hash: adb93122cbf753a26a0497479dbb88cf415de29bcommit hash: adb93122cbf753a26a0497479dbb88cf415de29bcommit hash: adb93122cbf753a26a0497479dbb88cf415de29bcommit hash: adb93122cbf753a26a0497479dbb88cf415de29b files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Deorbit RESTRICTED && NO_CDROM, part one.

For ports that already use the licenses framwork, merge the content of
RESTRICTED/NO_CDROM/LEGAL* entries into LICENSEs.

Approved by:	rene
Differential Revision:	https://reviews.freebsd.org/D30010
413
25 Apr 2021 17:18:38
commit hash: 6b63ef7436c4e0ec7693779240f1c90fa6e57a57commit hash: 6b63ef7436c4e0ec7693779240f1c90fa6e57a57commit hash: 6b63ef7436c4e0ec7693779240f1c90fa6e57a57commit hash: 6b63ef7436c4e0ec7693779240f1c90fa6e57a57 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/ucsc-userapps: Command line tools from the UCSC Genome Browser project

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.

Number of commits found: 14