notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)

/commits.php is going away

I'm proposing to take /commits.php away - it mainly duplicates the home page. Details in this GitHub issue.
Port details
ucsc-userapps Command line tools from the UCSC Genome Browser project
414_1 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 View this port on Repology. pkg-fallout 414Version of this port present on the latest quarterly branch.
Restricted RESTRICTED: Redistribution is limited, see license
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-04-25 17:21:12
Last Update: 2021-09-24 21:53:30
Commit Hash: d94f19a
Also Listed In: perl5 python
License: UCSC-GB
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (143 items)
Collapse this list.
  1. /usr/local/share/licenses/ucsc-userapps-414_1/catalog.mk
  2. /usr/local/share/licenses/ucsc-userapps-414_1/LICENSE
  3. /usr/local/share/licenses/ucsc-userapps-414_1/UCSC-GB
  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/bedClip
  12. userapps/bin/bedCommonRegions
  13. userapps/bin/bedGeneParts
  14. userapps/bin/bedGraphPack
  15. userapps/bin/bedGraphToBigWig
  16. userapps/bin/bedJoinTabOffset
  17. userapps/bin/bedPileUps
  18. userapps/bin/bedRemoveOverlap
  19. userapps/bin/bedRestrictToPositions
  20. userapps/bin/bedToBigBed
  21. userapps/bin/bigBedInfo
  22. userapps/bin/bigBedNamedItems
  23. userapps/bin/bigBedSummary
  24. userapps/bin/bigBedToBed
  25. userapps/bin/bigWigAverageOverBed
  26. userapps/bin/bigWigCat
  27. userapps/bin/bigWigCluster
  28. userapps/bin/bigWigCorrelate
  29. userapps/bin/bigWigInfo
  30. userapps/bin/bigWigMerge
  31. userapps/bin/bigWigSummary
  32. userapps/bin/bigWigToBedGraph
  33. userapps/bin/bigWigToWig
  34. userapps/bin/calc
  35. userapps/bin/catDir
  36. userapps/bin/catUncomment
  37. userapps/bin/ccCp
  38. userapps/bin/chopFaLines
  39. userapps/bin/clusterMatrixToBarChartBed
  40. userapps/bin/colTransform
  41. userapps/bin/convolve
  42. userapps/bin/countChars
  43. userapps/bin/cpg_lh
  44. userapps/bin/detab
  45. userapps/bin/dnsInfo
  46. userapps/bin/endsInLf
  47. userapps/bin/faAlign
  48. userapps/bin/faCmp
  49. userapps/bin/faCount
  50. userapps/bin/faFilter
  51. userapps/bin/faFilterN
  52. userapps/bin/faFlyBaseToUcsc
  53. userapps/bin/faFrag
  54. userapps/bin/faGapLocs
  55. userapps/bin/faGapSizes
  56. userapps/bin/faNcbiToUcsc
  57. userapps/bin/faNoise
  58. userapps/bin/faOneRecord
  59. userapps/bin/faPolyASizes
  60. userapps/bin/faRandomize
  61. userapps/bin/faRc
  62. userapps/bin/faRenameRecords
  63. userapps/bin/faSimplify
  64. userapps/bin/faSize
  65. userapps/bin/faSomeRecords
  66. userapps/bin/faSplit
  67. userapps/bin/faToFastq
  68. userapps/bin/faToNib
  69. userapps/bin/faToTab
  70. userapps/bin/faToTwoBit
  71. userapps/bin/faTrans
  72. userapps/bin/faTrimPolyA
  73. userapps/bin/faTrimRead
  74. userapps/bin/fastqStatsAndSubsample
  75. userapps/bin/fastqToFa
  76. userapps/bin/findMotif
  77. userapps/bin/fixCr
  78. userapps/bin/gapSplit
  79. userapps/bin/gffPeek
  80. userapps/bin/git-reports
  81. userapps/bin/gmtime
  82. userapps/bin/headRest
  83. userapps/bin/htmlCheck
  84. userapps/bin/htmlPics
  85. userapps/bin/jkUniq
  86. userapps/bin/lineCount
  87. userapps/bin/linesToRa
  88. userapps/bin/localtime
  89. userapps/bin/mktime
  90. userapps/bin/newProg
  91. userapps/bin/newPythonProg
  92. userapps/bin/nibFrag
  93. userapps/bin/nibSize
  94. userapps/bin/nt4Frag
  95. userapps/bin/paraFetch
  96. userapps/bin/paraSync
  97. userapps/bin/pslLiftSubrangeBlat
  98. userapps/bin/pslPosTarget
  99. userapps/bin/pslRemoveFrameShifts
  100. userapps/bin/pslScore
  101. userapps/bin/pslToPslx
  102. userapps/bin/pslToXa
  103. userapps/bin/raSqlQuery
  104. userapps/bin/raToLines
  105. userapps/bin/raToTab
  106. userapps/bin/randomLines
  107. userapps/bin/rmFaDups
  108. userapps/bin/rowsToCols
  109. userapps/bin/scaffoldFaToAgp
  110. userapps/bin/scrambleFa
  111. userapps/bin/sizeof
  112. userapps/bin/spacedToTab
  113. userapps/bin/splitFile
  114. userapps/bin/splitFileByColumn
  115. userapps/bin/strexCalc
  116. userapps/bin/stringify
  117. userapps/bin/subChar
  118. userapps/bin/subColumn
  119. userapps/bin/subs
  120. userapps/bin/tableSum
  121. userapps/bin/tailLines
  122. userapps/bin/textHist2
  123. userapps/bin/textHistogram
  124. userapps/bin/tickToDate
  125. userapps/bin/toLower
  126. userapps/bin/toUpper
  127. userapps/bin/trackDbIndexBb
  128. userapps/bin/twoBitDup
  129. userapps/bin/twoBitInfo
  130. userapps/bin/twoBitToFa
  131. userapps/bin/udcCleanup
  132. userapps/bin/undupFa
  133. userapps/bin/upper
  134. userapps/bin/vcfFilter
  135. userapps/bin/venn
  136. userapps/bin/verticalSplitSqlTable
  137. userapps/bin/weedLines
  138. userapps/bin/wigCorrelate
  139. userapps/bin/wigToBigWig
  140. userapps/bin/wordLine
  141. @owner
  142. @group
  143. @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
A package is not available for ports marked as: Forbidden / Broken / Ignore / Restricted
PKGNAME: there is no package for this port: _LICENSE_RESTRICTED = delete-package delete-distfiles
Flavors: there is no flavor information for this port.
ONLY_FOR_ARCHS: amd64
distinfo:
No package information for this port in our database

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. bash : shells/bash
  2. gmake>=4.3 : devel/gmake
  3. python3.8 : lang/python38
  4. perl5>=5.32.r0<5.33 : lang/perl5.32
Runtime dependencies:
  1. bash : shells/bash
  2. python3.8 : lang/python38
  3. perl5>=5.32.r0<5.33 : lang/perl5.32
Library dependencies:
  1. libiconv.so : converters/libiconv
  2. libmysqlclient.so : databases/mysql57-client
  3. libpng.so : graphics/png
There are no ports dependent upon this port

Configuration Options:
Options name:

USES:

pkg-message:
If installing:
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/
Collapse this list.

Number of commits found: 4

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
24 Sep 2021 21:53:30
 files touched by this commit commit hash:d94f19ab9ffcd2fac7650802d6aea3f68156f5d7  414_1
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]
15 May 2021 15:23:08
 files touched by this commit commit hash:43397d188c684b83c4bff3e9b78862a1f6ab47f7  414
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.
06 May 2021 11:47:41
 files touched by this commit commit hash:adb93122cbf753a26a0497479dbb88cf415de29b  413
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
25 Apr 2021 17:18:38
 files touched by this commit commit hash:6b63ef7436c4e0ec7693779240f1c90fa6e57a57  413
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: 4