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Port details
tRNAscan-SE Searching for tRNA genes in genomic sequence
2.0.0_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
2.0.0Version of this port present on the latest quarterly branch.
Maintainer: mzaki@niid.go.jp search for ports maintained by this maintainer
Port Added: 2002-03-27 14:19:04
Last Update: 2019-05-07 20:45:17
SVN Revision: 500976
License: GPLv3+
tRNAscan-SE was written in the PERL (version 5.0) script language.
Input consists of DNA or RNA sequences in FASTA format.  tRNA
predictions are output in standard tabular or ACeDB format.
tRNAscan-SE does no tRNA detection itself, but instead combines the
strengths of three independent tRNA prediction programs by negotiating
the flow of information between them, performing a limited amount of
post-processing, and outputting the results in one of several
formats.

WWW: http://lowelab.ucsc.edu/tRNAscan-SE/
SVNWeb : Homepage
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (139 items)
  1. /usr/local/share/licenses/tRNAscan-SE-2.0.0_1/catalog.mk
  2. /usr/local/share/licenses/tRNAscan-SE-2.0.0_1/LICENSE
  3. /usr/local/share/licenses/tRNAscan-SE-2.0.0_1/GPLv3+
  4. bin/EukHighConfidenceFilter
  5. bin/covels-SE
  6. bin/coves-SE
  7. bin/eufindtRNA
  8. bin/fasta2gsi
  9. bin/sstofa
  10. bin/tRNAscan-SE
  11. bin/trnascan-1.4
  12. etc/tRNAscan-SE.conf
  13. share/tRNAscan-SE/gcode/gcode.cilnuc
  14. share/tRNAscan-SE/gcode/gcode.echdmito
  15. share/tRNAscan-SE/gcode/gcode.invmito
  16. share/tRNAscan-SE/gcode/gcode.othmito
  17. share/tRNAscan-SE/gcode/gcode.vertmito
  18. share/tRNAscan-SE/gcode/gcode.ystmito
  19. share/tRNAscan-SE/models/Cren-eury-BHB-noncan.cm
  20. share/tRNAscan-SE/models/Dsignal
  21. share/tRNAscan-SE/models/ESELC.cm
  22. share/tRNAscan-SE/models/PSELC.cm
  23. share/tRNAscan-SE/models/TPCsignal
  24. share/tRNAscan-SE/models/TRNA2-arch.cm
  25. share/tRNAscan-SE/models/TRNA2-archns.cm
  26. share/tRNAscan-SE/models/TRNA2-bact.cm
  27. share/tRNAscan-SE/models/TRNA2-bactns.cm
  28. share/tRNAscan-SE/models/TRNA2-euk.cm
  29. share/tRNAscan-SE/models/TRNA2-eukns.cm
  30. share/tRNAscan-SE/models/TRNA2.cm
  31. share/tRNAscan-SE/models/TRNA2ns.cm
  32. share/tRNAscan-SE/models/TRNAinf-1415-ns.cm
  33. share/tRNAscan-SE/models/TRNAinf-1415.cm
  34. share/tRNAscan-SE/models/TRNAinf-arch-3h.cm
  35. share/tRNAscan-SE/models/TRNAinf-arch-5h.cm
  36. share/tRNAscan-SE/models/TRNAinf-arch-SeC.cm
  37. share/tRNAscan-SE/models/TRNAinf-arch-iso
  38. share/tRNAscan-SE/models/TRNAinf-arch-iso.i1f
  39. share/tRNAscan-SE/models/TRNAinf-arch-iso.i1i
  40. share/tRNAscan-SE/models/TRNAinf-arch-iso.i1m
  41. share/tRNAscan-SE/models/TRNAinf-arch-iso.i1p
  42. share/tRNAscan-SE/models/TRNAinf-arch-ns.cm
  43. share/tRNAscan-SE/models/TRNAinf-arch.cm
  44. share/tRNAscan-SE/models/TRNAinf-bact-SeC.cm
  45. share/tRNAscan-SE/models/TRNAinf-bact-iso
  46. share/tRNAscan-SE/models/TRNAinf-bact-iso.i1f
  47. share/tRNAscan-SE/models/TRNAinf-bact-iso.i1i
  48. share/tRNAscan-SE/models/TRNAinf-bact-iso.i1m
  49. share/tRNAscan-SE/models/TRNAinf-bact-iso.i1p
  50. share/tRNAscan-SE/models/TRNAinf-bact-ns.cm
  51. share/tRNAscan-SE/models/TRNAinf-bact.cm
  52. share/tRNAscan-SE/models/TRNAinf-euk-SeC.cm
  53. share/tRNAscan-SE/models/TRNAinf-euk-iso
  54. share/tRNAscan-SE/models/TRNAinf-euk-iso.i1f
  55. share/tRNAscan-SE/models/TRNAinf-euk-iso.i1i
  56. share/tRNAscan-SE/models/TRNAinf-euk-iso.i1m
  57. share/tRNAscan-SE/models/TRNAinf-euk-iso.i1p
  58. share/tRNAscan-SE/models/TRNAinf-euk-ns.cm
  59. share/tRNAscan-SE/models/TRNAinf-euk.cm
  60. share/tRNAscan-SE/models/TRNAinf-mito-mammal
  61. share/tRNAscan-SE/models/TRNAinf-mito-mammal-Ala.cm
  62. share/tRNAscan-SE/models/TRNAinf-mito-mammal-Arg.cm
  63. share/tRNAscan-SE/models/TRNAinf-mito-mammal-Asn.cm
  64. share/tRNAscan-SE/models/TRNAinf-mito-mammal-Asp.cm
  65. share/tRNAscan-SE/models/TRNAinf-mito-mammal-Cys.cm
  66. share/tRNAscan-SE/models/TRNAinf-mito-mammal-Gln.cm
  67. share/tRNAscan-SE/models/TRNAinf-mito-mammal-Glu.cm
  68. share/tRNAscan-SE/models/TRNAinf-mito-mammal-Gly.cm
  69. share/tRNAscan-SE/models/TRNAinf-mito-mammal-His.cm
  70. share/tRNAscan-SE/models/TRNAinf-mito-mammal-Ile.cm
  71. share/tRNAscan-SE/models/TRNAinf-mito-mammal-LeuTAA.cm
  72. share/tRNAscan-SE/models/TRNAinf-mito-mammal-LeuTAG.cm
  73. share/tRNAscan-SE/models/TRNAinf-mito-mammal-Lys.cm
  74. share/tRNAscan-SE/models/TRNAinf-mito-mammal-Met.cm
  75. share/tRNAscan-SE/models/TRNAinf-mito-mammal-Phe.cm
  76. share/tRNAscan-SE/models/TRNAinf-mito-mammal-Pro.cm
  77. share/tRNAscan-SE/models/TRNAinf-mito-mammal-SerGCT.cm
  78. share/tRNAscan-SE/models/TRNAinf-mito-mammal-SerTGA.cm
  79. share/tRNAscan-SE/models/TRNAinf-mito-mammal-Thr.cm
  80. share/tRNAscan-SE/models/TRNAinf-mito-mammal-Trp.cm
  81. share/tRNAscan-SE/models/TRNAinf-mito-mammal-Tyr.cm
  82. share/tRNAscan-SE/models/TRNAinf-mito-mammal-Val.cm
  83. share/tRNAscan-SE/models/TRNAinf-mito-mammal.i1f
  84. share/tRNAscan-SE/models/TRNAinf-mito-mammal.i1i
  85. share/tRNAscan-SE/models/TRNAinf-mito-mammal.i1m
  86. share/tRNAscan-SE/models/TRNAinf-mito-mammal.i1p
  87. share/tRNAscan-SE/models/TRNAinf-mito-vert
  88. share/tRNAscan-SE/models/TRNAinf-mito-vert-Ala.cm
  89. share/tRNAscan-SE/models/TRNAinf-mito-vert-Arg.cm
  90. share/tRNAscan-SE/models/TRNAinf-mito-vert-Asn.cm
  91. share/tRNAscan-SE/models/TRNAinf-mito-vert-Asp.cm
  92. share/tRNAscan-SE/models/TRNAinf-mito-vert-Cys.cm
  93. share/tRNAscan-SE/models/TRNAinf-mito-vert-Gln.cm
  94. share/tRNAscan-SE/models/TRNAinf-mito-vert-Glu.cm
  95. share/tRNAscan-SE/models/TRNAinf-mito-vert-Gly.cm
  96. share/tRNAscan-SE/models/TRNAinf-mito-vert-His.cm
  97. share/tRNAscan-SE/models/TRNAinf-mito-vert-Ile.cm
  98. share/tRNAscan-SE/models/TRNAinf-mito-vert-LeuTAA.cm
  99. share/tRNAscan-SE/models/TRNAinf-mito-vert-LeuTAG.cm
  100. share/tRNAscan-SE/models/TRNAinf-mito-vert-Lys.cm
  101. share/tRNAscan-SE/models/TRNAinf-mito-vert-Met.cm
  102. share/tRNAscan-SE/models/TRNAinf-mito-vert-Phe.cm
  103. share/tRNAscan-SE/models/TRNAinf-mito-vert-Pro.cm
  104. share/tRNAscan-SE/models/TRNAinf-mito-vert-SerGCT.cm
  105. share/tRNAscan-SE/models/TRNAinf-mito-vert-SerTGA.cm
  106. share/tRNAscan-SE/models/TRNAinf-mito-vert-Thr.cm
  107. share/tRNAscan-SE/models/TRNAinf-mito-vert-Trp.cm
  108. share/tRNAscan-SE/models/TRNAinf-mito-vert-Tyr.cm
  109. share/tRNAscan-SE/models/TRNAinf-mito-vert-Val.cm
  110. share/tRNAscan-SE/models/TRNAinf-mito-vert.i1f
  111. share/tRNAscan-SE/models/TRNAinf-mito-vert.i1i
  112. share/tRNAscan-SE/models/TRNAinf-mito-vert.i1m
  113. share/tRNAscan-SE/models/TRNAinf-mito-vert.i1p
  114. share/tRNAscan-SE/models/TRNAinf-ns.cm
  115. share/tRNAscan-SE/models/TRNAinf.cm
  116. share/tRNAscan-SE/models/Thaum-BHB-noncan.cm
  117. share/tRNAscan-SE/tRNAscanSE/ArrayCMscanResults.pm
  118. share/tRNAscan-SE/tRNAscanSE/ArraytRNA.pm
  119. share/tRNAscan-SE/tRNAscanSE/CM.pm
  120. share/tRNAscan-SE/tRNAscanSE/CMscanResultFile.pm
  121. share/tRNAscan-SE/tRNAscanSE/Configuration.pm
  122. share/tRNAscan-SE/tRNAscanSE/Eufind.pm
  123. share/tRNAscan-SE/tRNAscanSE/FpScanResultFile.pm
  124. share/tRNAscan-SE/tRNAscanSE/GeneticCode.pm
  125. share/tRNAscan-SE/tRNAscanSE/IntResultFile.pm
  126. share/tRNAscan-SE/tRNAscanSE/LogFile.pm
  127. share/tRNAscan-SE/tRNAscanSE/MultiResultFile.pm
  128. share/tRNAscan-SE/tRNAscanSE/Options.pm
  129. share/tRNAscan-SE/tRNAscanSE/ResultFileReader.pm
  130. share/tRNAscan-SE/tRNAscanSE/SS.pm
  131. share/tRNAscan-SE/tRNAscanSE/ScanResult.pm
  132. share/tRNAscan-SE/tRNAscanSE/Sequence.pm
  133. share/tRNAscan-SE/tRNAscanSE/SprinzlAlign.pm
  134. share/tRNAscan-SE/tRNAscanSE/SprinzlAlignResults.pm
  135. share/tRNAscan-SE/tRNAscanSE/SprinzlPos.pm
  136. share/tRNAscan-SE/tRNAscanSE/Stats.pm
  137. share/tRNAscan-SE/tRNAscanSE/Tscan.pm
  138. share/tRNAscan-SE/tRNAscanSE/Utils.pm
  139. share/tRNAscan-SE/tRNAscanSE/tRNA.pm
  140. Collapse this list.
Dependency lines:
  • tRNAscan-SE>0:biology/tRNAscan-SE

To install the port: cd /usr/ports/biology/tRNAscan-SE/ && make install clean
To add the package: pkg install tRNAscan-SE

PKGNAME: tRNAscan-SE

There is no flavor information for this port.

distinfo:

TIMESTAMP = 1528270436
SHA256 (trnascan-se-2.0.0.tar.gz) = 0dde1c07142e4bf77b21d53ddf3eeb1ef8c52248005a42323d13f8d7c798100c
SIZE (trnascan-se-2.0.0.tar.gz) = 4372755


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. autoconf>=2.69 : devel/autoconf
  2. automake>=1.16.1 : devel/automake
  3. perl5>=5.28.r1<5.29 : lang/perl5.28
Runtime dependencies:
  1. cmsearch : biology/infernal
  2. perl5>=5.28.r1<5.29 : lang/perl5.28
There are no ports dependent upon this port

Configuration Options
     No options to configure

USES:
compiler:c11 perl5 autoreconf

Master Sites:
  1. http://lowelab.ucsc.edu/software/

Number of commits found: 23

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
07 May 2019 19:45:17
Original commit files touched by this commit  2.0.0_1
Revision:500976
pkubaj search for other commits by this committer
biology/tRNAscan-SE: fix build with GCC-based architectures

Add USES=compiler:c11 to fix build.

Approved by:	mentors (implicit approval)
28 Sep 2018 00:12:49
Original commit files touched by this commit  2.0.0_1
Revision:480837
wen search for other commits by this committer
- Unbreak by adding missing pkg-plist

PR:		228758
Submitted by:	mzaki@niid.go.jp(maintainer)
29 Jun 2018 12:43:20
Original commit files touched by this commit  2.0.0_1
Revision:473544
antoine search for other commits by this committer
Mark BROKEN: missing plist
06 Jun 2018 15:20:57
Original commit files touched by this commit  2.0.0
Revision:471852
krion search for other commits by this committer
Update to 2.0.0 and pass maintainership to committer.

PR:		228758
Submitted by:	Motomichi Matsuzaki <mzaki@niid.go.jp>
05 May 2018 10:49:36
Original commit files touched by this commit  1.23_1
Revision:469100
antoine search for other commits by this committer
Deprecate ports broken for more than 6 months
13 Oct 2017 11:14:53
Original commit files touched by this commit  1.23_1
Revision:451982  Sanity Test Failure
bapt search for other commits by this committer
Mark as broken ports with no public distfiles
13 May 2016 18:38:34
Original commit files touched by this commit  1.23_1
Revision:415128
bapt search for other commits by this committer
Prevent collision with getline(3)
29 Jul 2014 19:11:53
Original commit files touched by this commit  1.23_1
Revision:363374
adamw search for other commits by this committer
Convert a bunch of EXTRACT_SUFX=... into USES=tar:...

Approved by:	portmgr (not really, but touches unstaged ports)
05 May 2014 10:26:16
Original commit files touched by this commit  1.23_1
Revision:352989
bapt search for other commits by this committer
Support stage
05 Feb 2014 23:44:50
Original commit files touched by this commit  1.23_1
Revision:342905
marino search for other commits by this committer
biology/tRNAscan-SE: Fix hardcoded perl path
20 Sep 2013 15:55:44
Original commit files touched by this commit  1.23_1
Revision:327709
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
03 Aug 2013 08:45:52
Original commit files touched by this commit  1.23_1
Revision:324181
az search for other commits by this committer
- Convert to new perl framework
- Trim Makefile header
19 Jun 2013 19:20:26
Original commit files touched by this commit  1.23_1
Revision:321314
bsam search for other commits by this committer
. NOPORTDOCS -> PORT_OPTIONS:MDOCS;
. pet portlint: use {} instaed of () at variable;
. use PLIST_FILES, PORTDATA and PORTDOCS at Makefile;
. get rid of pkg-plist;
. remove article from COMMENT;
. trim Makefile headers.
19 Mar 2011 12:38:54
Original commit files touched by this commit  1.23_1

miwi search for other commits by this committer
- Get Rid MD5 support
22 May 2008 00:49:42
Original commit files touched by this commit  1.23_1

miwi search for other commits by this committer
- Update MASTER_SITES and WWW: line
- Support CC/CFLAGS properly
- Strip binary

PR:             123866
Submitted by:   Ports Fury
15 May 2008 02:50:22
Original commit files touched by this commit  1.23

erwin search for other commits by this committer
Update to 1.23
10 Mar 2007 20:20:10
Original commit files touched by this commit  1.21

linimon search for other commits by this committer
Reset chuynh@biolateral.com.au: address bounces.

Hat:            portmgr
22 Jan 2006 08:20:34
Original commit files touched by this commit  1.21

edwin search for other commits by this committer
SHA256ify

Approved by:    krion@
31 Mar 2004 03:12:58
Original commit files touched by this commit  1.21

trevor search for other commits by this committer
SIZEify (maintainer timeout)
22 Oct 2003 09:29:55
Original commit files touched by this commit  1.21

osa search for other commits by this committer
Cosmetic fix: use %%DOCSDIR%% macro.
No functionally changes.

Submitted by:   Oleg Karachevtsev <ok@etrust.ru>
A part of PR:   57992
21 Feb 2003 11:01:38
Original commit files touched by this commit  1.21

knu search for other commits by this committer
De-pkg-comment.
04 Nov 2002 01:47:57
Original commit files touched by this commit  1.21

edwin search for other commits by this committer
Port needs perl to build.
Seen on: bento
27 Mar 2002 14:18:50
Original commit files touched by this commit  1.21

wjv search for other commits by this committer
Add tRNAscan-SE 1.21, an improved tool for transfer RNA detection.

PR:             33853
Submitted by:   chuynh@biolateral.com.au

Number of commits found: 23

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