notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)
Want a good monitor light? See my photosAll times are UTC
Ukraine
This referral link gives you 10% off a Fastmail.com account and gives me a discount on my Fastmail account.

Get notified when packages are built

A new feature has been added. FreshPorts already tracks package built by the FreeBSD project. This information is displayed on each port page. You can now get an email when FreshPorts notices a new package is available for something on one of your watch lists. However, you must opt into that. Click on Report Subscriptions on the right, and New Package Notification box, and click on Update.

Finally, under Watch Lists, click on ABI Package Subscriptions to select your ABI (e.g. FreeBSD:14:amd64) & package set (latest/quarterly) combination for a given watch list. This is what FreshPorts will look for.

Port details on branch 2022Q3
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 414_1Version 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: 2023-12-30 07:16:41
Commit Hash: 9ee2e86
Also Listed In: perl5 python
License: UCSC-GB
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 (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
We doubt a package is available for this port because we see it marked as as:
  • Restricted
  • Package not available
Packages are normally not provided for ports that are marked as above.
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: 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:
TIMESTAMP = 1621027743 SHA256 (userApps.v414.src.tgz) = 36910b5c84ea613d4eb6ccb9572f3b34d929c5571578b1d91013391895638ab0 SIZE (userApps.v414.src.tgz) = 19195157

No package information for this port in our database
Sometimes this happens. Not all ports have packages.
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. python3.9 : lang/python39
  4. perl5>=5.36<5.37 : lang/perl5.36
Test dependencies:
  1. python3.9 : lang/python39
Runtime dependencies:
  1. bash : shells/bash
  2. python3.9 : lang/python39
  3. perl5>=5.36<5.37 : lang/perl5.36
Library dependencies:
  1. libiconv.so : converters/libiconv
  2. libpng.so : graphics/png
  3. libmysqlclient.so.21 : databases/mysql80-client
There are no ports dependent upon this port

Configuration Options:
No options to configure
Options name:
biology_ucsc-userapps
USES:
gmake localbase:ldflags mysql shebangfix perl5 python 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. http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/
Collapse this list.

There are no commits on branch 2022Q3 for this port