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Port details
seqtools Tools for visualising sequence alignments
4.44.1_4 biology Deleted 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 4.44.1_4Version of this port present on the latest quarterly branch.
Broken BROKEN: unfetchable
Deprecated DEPRECATED: Broken for more than 6 months
Expired This port expired on: 2020-05-05
Ignore IGNORE: is marked as broken: unfetchable
Maintainer: pi@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2013-11-10 11:01:14
Last Update: 2020-05-05 15:38:12
SVN Revision: 534093
License: GPLv3
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (229 items)
Collapse this list.
  1. /usr/local/share/licenses/seqtools-4.44.1_4/catalog.mk
  2. /usr/local/share/licenses/seqtools-4.44.1_4/LICENSE
  3. /usr/local/share/licenses/seqtools-4.44.1_4/GPLv3
  4. share/doc/seqtools/Belvu_manual.pdf
  5. share/doc/seqtools/Blixem_manual.pdf
  6. share/doc/seqtools/Dotter_manual.pdf
  7. share/doc/seqtools/belvu_quick_start.html
  8. share/doc/seqtools/belvu_usage.txt
  9. share/doc/seqtools/blixem_quick_start.html
  10. share/doc/seqtools/blixem_usage.txt
  11. share/doc/seqtools/dotter_quick_start.html
  12. share/doc/seqtools/dotter_usage.txt
  13. share/doc/seqtools/release_notes.html
  14. share/doc/seqtools/todo.html
  15. bin/belvu
  16. bin/blixem
  17. bin/blixemh
  18. bin/dotter
  19. include/blatSrc/ace.h
  20. include/blatSrc/aliType.h
  21. include/blatSrc/annoAssembly.h
  22. include/blatSrc/annoFilter.h
  23. include/blatSrc/annoFormatTab.h
  24. include/blatSrc/annoFormatter.h
  25. include/blatSrc/annoGrateWig.h
  26. include/blatSrc/annoGrator.h
  27. include/blatSrc/annoGratorQuery.h
  28. include/blatSrc/annoOption.h
  29. include/blatSrc/annoRow.h
  30. include/blatSrc/annoStreamBigBed.h
  31. include/blatSrc/annoStreamBigWig.h
  32. include/blatSrc/annoStreamTab.h
  33. include/blatSrc/annoStreamVcf.h
  34. include/blatSrc/annoStreamer.h
  35. include/blatSrc/apacheLog.h
  36. include/blatSrc/asParse.h
  37. include/blatSrc/axt.h
  38. include/blatSrc/bPlusTree.h
  39. include/blatSrc/bamFile.h
  40. include/blatSrc/bandExt.h
  41. include/blatSrc/base64.h
  42. include/blatSrc/basicBed.h
  43. include/blatSrc/bbiFile.h
  44. include/blatSrc/bigBed.h
  45. include/blatSrc/bigWig.h
  46. include/blatSrc/binRange.h
  47. include/blatSrc/bits.h
  48. include/blatSrc/blastParse.h
  49. include/blatSrc/boxClump.h
  50. include/blatSrc/boxLump.h
  51. include/blatSrc/bwgInternal.h
  52. include/blatSrc/cda.h
  53. include/blatSrc/cgi_build_rules.mk
  54. include/blatSrc/chain.h
  55. include/blatSrc/chainBlock.h
  56. include/blatSrc/chainConnect.h
  57. include/blatSrc/chainToAxt.h
  58. include/blatSrc/chainToPsl.h
  59. include/blatSrc/cheapcgi.h
  60. include/blatSrc/cirTree.h
  61. include/blatSrc/codebias.h
  62. include/blatSrc/common.h
  63. include/blatSrc/common.mk
  64. include/blatSrc/correlate.h
  65. include/blatSrc/crTree.h
  66. include/blatSrc/crudeali.h
  67. include/blatSrc/diGraph.h
  68. include/blatSrc/diGraph.h.97
  69. include/blatSrc/dlist.h
  70. include/blatSrc/dnaLoad.h
  71. include/blatSrc/dnaMarkov.h
  72. include/blatSrc/dnaMotif.h
  73. include/blatSrc/dnaseq.h
  74. include/blatSrc/dnautil.h
  75. include/blatSrc/dtdParse.h
  76. include/blatSrc/dyOut.h
  77. include/blatSrc/dystring.h
  78. include/blatSrc/elmTree.h
  79. include/blatSrc/emblParse.h
  80. include/blatSrc/ens.h
  81. include/blatSrc/errAbort.h
  82. include/blatSrc/errCatch.h
  83. include/blatSrc/fa.h
  84. include/blatSrc/fieldedTable.h
  85. include/blatSrc/filePath.h
  86. include/blatSrc/flydna.h
  87. include/blatSrc/fof.h
  88. include/blatSrc/fq.h
  89. include/blatSrc/fuzzyFind.h
  90. include/blatSrc/gapCalc.h
  91. include/blatSrc/gdf.h
  92. include/blatSrc/genoFind.h
  93. include/blatSrc/genomeRangeTree.h
  94. include/blatSrc/gfClientLib.h
  95. include/blatSrc/gfPcrLib.h
  96. include/blatSrc/gfWebLib.h
  97. include/blatSrc/gff.h
  98. include/blatSrc/gff3.h
  99. include/blatSrc/gfxPoly.h
  100. include/blatSrc/gifLabel.h
  101. include/blatSrc/hacTree.h
  102. include/blatSrc/hash.h
  103. include/blatSrc/hex.h
  104. include/blatSrc/hgGene.h
  105. include/blatSrc/hgap.h
  106. include/blatSrc/hgdb.h
  107. include/blatSrc/histogram.h
  108. include/blatSrc/hmac.h
  109. include/blatSrc/hmmPfamParse.h
  110. include/blatSrc/hmmstats.h
  111. include/blatSrc/htmlPage.h
  112. include/blatSrc/htmshell.h
  113. include/blatSrc/https.h
  114. include/blatSrc/intValTree.h
  115. include/blatSrc/internet.h
  116. include/blatSrc/itsa.h
  117. include/blatSrc/iupac.h
  118. include/blatSrc/jointalign.h
  119. include/blatSrc/jpegSize.h
  120. include/blatSrc/jsonParse.h
  121. include/blatSrc/jsonWrite.h
  122. include/blatSrc/keys.h
  123. include/blatSrc/knetUdc.h
  124. include/blatSrc/kxTok.h
  125. include/blatSrc/linefile.h
  126. include/blatSrc/localEnvironment.mk
  127. include/blatSrc/localmem.h
  128. include/blatSrc/log.h
  129. include/blatSrc/longToList.h
  130. include/blatSrc/maDbRep.h
  131. include/blatSrc/maToFf.h
  132. include/blatSrc/maf.h
  133. include/blatSrc/mailViaPipe.h
  134. include/blatSrc/md5.h
  135. include/blatSrc/memalloc.h
  136. include/blatSrc/memgfx.h
  137. include/blatSrc/meta.h
  138. include/blatSrc/metaWig.h
  139. include/blatSrc/mime.h
  140. include/blatSrc/net.h
  141. include/blatSrc/nib.h
  142. include/blatSrc/nibTwo.h
  143. include/blatSrc/nt4.h
  144. include/blatSrc/obscure.h
  145. include/blatSrc/oldGff.h
  146. include/blatSrc/oligoTm.h
  147. include/blatSrc/ooc.h
  148. include/blatSrc/options.h
  149. include/blatSrc/pairDistance.h
  150. include/blatSrc/pairHmm.h
  151. include/blatSrc/paraFetch.h
  152. include/blatSrc/patSpace.h
  153. include/blatSrc/peakCluster.h
  154. include/blatSrc/phyloTree.h
  155. include/blatSrc/pipeline.h
  156. include/blatSrc/portable.h
  157. include/blatSrc/psGfx.h
  158. include/blatSrc/psPoly.h
  159. include/blatSrc/pscmGfx.h
  160. include/blatSrc/psl.h
  161. include/blatSrc/pslTbl.h
  162. include/blatSrc/pslTransMap.h
  163. include/blatSrc/pthreadDoList.h
  164. include/blatSrc/pthreadWrap.h
  165. include/blatSrc/qa.h
  166. include/blatSrc/quickHeap.h
  167. include/blatSrc/quotedP.h
  168. include/blatSrc/ra.h
  169. include/blatSrc/raToStruct.h
  170. include/blatSrc/rainbow.h
  171. include/blatSrc/rangeTree.h
  172. include/blatSrc/rbTree.h
  173. include/blatSrc/regexHelper.h
  174. include/blatSrc/repMask.h
  175. include/blatSrc/rle.h
  176. include/blatSrc/rnautil.h
  177. include/blatSrc/rql.h
  178. include/blatSrc/rudp.h
  179. include/blatSrc/scoreWindow.h
  180. include/blatSrc/seg.h
  181. include/blatSrc/seqOut.h
  182. include/blatSrc/seqStats.h
  183. include/blatSrc/shaRes.h
  184. include/blatSrc/sig.h
  185. include/blatSrc/slog.h
  186. include/blatSrc/snof.h
  187. include/blatSrc/snofmake.h
  188. include/blatSrc/spaceSaver.h
  189. include/blatSrc/spacedColumn.h
  190. include/blatSrc/spacedSeed.h
  191. include/blatSrc/splatAli.h
  192. include/blatSrc/splix.h
  193. include/blatSrc/sqlList.h
  194. include/blatSrc/sqlNum.h
  195. include/blatSrc/subText.h
  196. include/blatSrc/sufa.h
  197. include/blatSrc/sufx.h
  198. include/blatSrc/supStitch.h
  199. include/blatSrc/synQueue.h
  200. include/blatSrc/tabRow.h
  201. include/blatSrc/textOut.h
  202. include/blatSrc/tokenizer.h
  203. include/blatSrc/trans3.h
  204. include/blatSrc/trix.h
  205. include/blatSrc/twoBit.h
  206. include/blatSrc/udc.h
  207. include/blatSrc/unfin.h
  208. include/blatSrc/userApp.mk
  209. include/blatSrc/vGfx.h
  210. include/blatSrc/vcf.h
  211. include/blatSrc/vcfBits.h
  212. include/blatSrc/verbose.h
  213. include/blatSrc/wormdna.h
  214. include/blatSrc/xAli.h
  215. include/blatSrc/xa.h
  216. include/blatSrc/xap.h
  217. include/blatSrc/xenalign.h
  218. include/blatSrc/xmlEscape.h
  219. include/blatSrc/xp.h
  220. include/blatSrc/zlibFace.h
  221. include/gbtools/gbtools.hpp
  222. include/gbtools/gbtoolsCurl.hpp
  223. include/gbtools/gbtoolsGUI.hpp
  224. include/gbtools/gbtoolsPfetch.hpp
  225. include/gbtools/gbtoolsTrackhub.hpp
  226. include/gbtools/gbtoolsUtils.hpp
  227. include/json/json-forwards.h
  228. include/json/json.h
  229. lib/libgbtools.a
Collapse this list.
Dependency lines:
  • seqtools>0:biology/seqtools
No installation instructions: this port has been deleted.
The package name of this deleted port was:
PKGNAME: seqtools
Flavors: there is no flavor information for this port.
distinfo:
Packages (timestamps in pop-ups are UTC):
seqtools
ABIlatestquarterly
FreeBSD:11:aarch644.44.1_2-
FreeBSD:11:amd64--
FreeBSD:11:armv64.42.1-
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch644.44.1_2-
FreeBSD:12:amd64--
FreeBSD:12:armv64.44.1_2-
FreeBSD:12:armv74.44.1_2-
FreeBSD:12:i386--
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64--
FreeBSD:13:amd64--
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i386--
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:14:aarch64--
FreeBSD:14:amd64--
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i386--
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. msgfmt : devel/gettext-tools
  2. pkgconf>=1.3.0_1 : devel/pkgconf
  3. as : devel/binutils
  4. x11.pc : x11/libX11
Runtime dependencies:
  1. x11.pc : x11/libX11
Library dependencies:
  1. libcurl.so : ftp/curl
  2. libsqlite3.so : databases/sqlite3
  3. libfontconfig.so : x11-fonts/fontconfig
  4. libfreetype.so : print/freetype2
  5. libintl.so : devel/gettext-runtime
  6. libatk-1.0.so : accessibility/atk
  7. libcairo.so : graphics/cairo
  8. libgdk_pixbuf-2.0.so : graphics/gdk-pixbuf2
  9. libglib-2.0.so : devel/glib20
  10. libintl.so : devel/gettext-runtime
  11. libgtk-x11-2.0.so : x11-toolkits/gtk20
  12. libpango-1.0.so : x11-toolkits/pango
There are no ports dependent upon this port

Configuration Options:
Options name:

USES:

Master Sites:
Expand this list (1 items)
Collapse this list.
  1. ftp://ftp.sanger.ac.uk/pub4/resources/software/seqtools/PRODUCTION/
Collapse this list.
Port Moves
  • port deleted on 2020-05-05
    REASON: Has expired: Broken for more than 6 months
  • port moved here from biology/dotter on 2013-11-10
    REASON: Replaced with biology/seqtools

Number of commits found: 44

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
05 May 2020 15:38:12
Original commit files touched by this commit Revision:534093  4.44.1_4
rene search for other commits by this committer
Remove expired ports:

Adjusted for ports rescued since r534032

2020-05-05 audio/festvox-czech: Broken for more than 6 months
2020-05-05 audio/gkrellmvolume2: Broken for more than 6 months
2020-05-05 audio/mixmos: Broken for more than 6 months
2020-05-05 audio/mma: Broken for more than 6 months
2020-05-05 audio/pd-cyclone: Broken for more than 6 months
2020-05-05 audio/shorten: Broken for more than 6 months
2020-05-05 audio/taglib-sharp: Broken for more than 6 months
2020-05-05 audio/xhippo: Broken for more than 6 months
2020-05-05 biology/consed: Broken for more than 6 months
2020-05-05 biology/plinkseq: Broken for more than 6 months
2020-05-05 biology/seqtools: Broken for more than 6 months
(Only the first 15 lines of the commit message are shown above View all of this commit message)
04 Apr 2020 20:51:41
Original commit files touched by this commit Revision:530719  4.44.1_4  Sanity Test Failure
antoine search for other commits by this committer
Deprecate ports broken for more than 6 months
06 Nov 2019 12:48:32
Original commit files touched by this commit Revision:516880  4.44.1_4  Sanity Test Failure
antoine search for other commits by this committer
Mark a few ports BROKEN, unfetchable
04 Nov 2019 21:08:20
Original commit files touched by this commit Revision:516742  4.44.1_4
zeising search for other commits by this committer
Add USES=xorg USES=gl, ports categories b

Add USES=xorg, USES=gl and in a few cases USES=gnome to ports in categories
starting with 'b'.
26 Jul 2019 20:46:57
Original commit files touched by this commit Revision:507372  4.44.1_4
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330
07 Jan 2019 19:54:40
Original commit files touched by this commit Revision:489613  4.44.1_3
pi search for other commits by this committer
biology/seqtools: fix build on current, if lld is lld7

- fixed by LLD_UNSAFE=yes

PR:		230609
Submitted by:	jbeich
12 Dec 2018 01:35:36
Original commit files touched by this commit Revision:487272  4.44.1_3
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590
12 Dec 2017 03:38:56
Original commit files touched by this commit Revision:456096  4.44.1_2
jbeich search for other commits by this committer
biology/seqtools: re-try on powerpc* after r449590
22 Sep 2017 10:48:29
Original commit files touched by this commit Revision:450351  4.44.1_2
mat search for other commits by this committer
Remove USES=execinfo.

PR:		220271
Submitted by:	mat (review), Yasuhiro KIMURA (PR)
Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D11488
10 Sep 2017 20:55:39
Original commit files touched by this commit Revision:449591  4.44.1_2
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
(via Mk/bsd.default-versions.mk and lang/gcc) which has moved from
GCC 5.4 to GCC 6.4 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++11-lang,
   c++14-lang, c++0x, c11, or gcc-c++11-lib.

PR:		219275
21 May 2017 21:55:08
Original commit files touched by this commit Revision:441429  4.44.1_1
linimon search for other commits by this committer
Mark some ports failing on power64.  In cases where the error message
was a stub, provide a real one.

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)
Reported by:	swills
01 Apr 2017 15:23:32
Original commit files touched by this commit Revision:437439  4.44.1_1
gerald search for other commits by this committer
Bump PORTREVISIONs for ports depending on the canonical version of GCC and
lang/gcc which have moved from GCC 4.9.4 to GCC 5.4 (at least under some
circumstances such as versions of FreeBSD or platforms).

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using using Mk/bsd.octave.mk which in turn has USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++14-lang,
   c++11-lang, c++0x, c11, or gcc-c++11-lib.

PR:		216707
01 Jan 2017 03:45:13
Original commit files touched by this commit Revision:430235  4.44.1
sunpoet search for other commits by this committer
Remove BROKEN_FreeBSD_9

Approved by:	portmgr (blanket)
11 Nov 2016 06:19:10
Original commit files touched by this commit Revision:425863  4.44.1
pi search for other commits by this committer
biology/seqtools: update 4.43.0 -> 4.44.1

- Blixem: Features can now be added to multiple different groups/filters.
- Belvu: Fix a problem where column highlighting can get out of sync
  with the text.
31 Jul 2016 14:19:09
Original commit files touched by this commit Revision:419380  4.43.0
pi search for other commits by this committer
biology/seqtools: 4.42.1 -> 4.43.0

 
ftp://ftp.sanger.ac.uk/pub4/resources/software/seqtools/PRODUCTION/release_notes.html

- Mark broken on 9.x: Fails to build due to C++ std issues
22 Apr 2016 16:27:25
Original commit files touched by this commit Revision:413787  4.42.1
pi search for other commits by this committer
biology/seqtools: 4.41.1 -> 4.42.1

- fixes build on 9.x
- Added a feedback box to show the read depth at the selected coord.
  Hover over this box to see the specific base support (i.e. the
  number of A/C/G/Ts).
01 Apr 2016 13:29:17
Original commit files touched by this commit Revision:412344  4.41.1
mat search for other commits by this committer
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
14 Mar 2016 19:40:34
Original commit files touched by this commit Revision:411109  4.41.1
pi search for other commits by this committer
biology/seqtools: 4.40.0 -> 4.41.1

- mostly internal changes, some build fixes
06 Feb 2016 10:17:31
Original commit files touched by this commit Revision:408287  4.40.0
pi search for other commits by this committer
biology/seqtools: 4.39.3 -> 4.40.0

- Blixem can now accept a 'command' tag in a gff line for a region
  feature. The given command should return gff and will be run by
  blixem on the given region.
- Blixem now supports fetching sequence data over https.
05 Dec 2015 13:20:21
Original commit files touched by this commit Revision:403064  4.39.3
pi search for other commits by this committer
biology/seqtools: 4.39.2 -> 4.39.3

- Blixem
  Further improve the display of features in the detail view
  when they have transparent fill, making sure that they have a
  visible border.
01 Dec 2015 20:50:34
Original commit files touched by this commit Revision:402787  4.39.2
pi search for other commits by this committer
biology/seqtools: 4.39.1 -> 4.39.2

- Blixem:
  Improve the display of features in the detail view when they
  have transparent fill.
18 Nov 2015 10:53:48
Original commit files touched by this commit Revision:401862  4.39.1
pi search for other commits by this committer
biology/seqtools: Fix distinfo, WWW

- Side effect of the seqtools automated build system

Submitted by:	pkg-fallout
13 Nov 2015 18:46:02
Original commit files touched by this commit Revision:401527  4.39.1
pi search for other commits by this committer
biology/seqtools: 4.39.0 -> 4.39.1

- Fix a bug in Belvu where the display was being initialised in
  command-line-only modes.
08 Nov 2015 16:39:58
Original commit files touched by this commit Revision:401065  4.39.0
pi search for other commits by this committer
biology/seqtools: 4.36 -> 4.39.0

- Blixem
  o There is now an optional setting to highlight "maybe-canonical"
    splice sites in Blixem. This can be used to help identify
    problems where the strand is incorrect in the input data - it
    highlights splice sites in a different colour if they would be
    canonical were they on the other strand.
  o Fixed a bug with colinearity lines when an alignment's cigar
    string contains introns.
  o There are now separate feedback boxes for the selected sequence
    name coordinates. Hover over each box to see a tooltip describing
    its contents.
08 Aug 2015 11:22:25
Original commit files touched by this commit Revision:393723  4.36
pi search for other commits by this committer
biology/seqtools: 4.35 -> 4.36

Minor under-the-hood changes
07 Jul 2015 14:17:52
Original commit files touched by this commit Revision:391503  4.35
pi search for other commits by this committer
biology/seqtools: 4.34.1 -> 4.35

- Blixem bug fix in sorting features, RT 473624
- Compilation of the seqtools in parallel, RT 467905
- Fix bug with sorting by similarity/identity to first sequence (RT:473624)
- Fix an error compiling with multiple threads (RT:467905)
06 May 2015 20:30:54
Original commit files touched by this commit Revision:385561  4.34.1
pi search for other commits by this committer
biology/seqtools: 4.33 -> 4.34.1

Blixem
- Added functionality to shift-select a range of coordinates,
  and copy the reference/match sequence for that range.
- DNA search now highlights the resultant range of coordinates.
- Added a splitter bar to allow the variations track to be resized.
- Dotter
  Fix a crash pressing Esc on an undocked alignment or greyramp tool.
- All
  Code reorganisation: the codebase is now in C++ rather than C,
  and a new module 'gbtools' has been created for generic
  utility functions.
31 Mar 2015 18:04:26
Original commit files touched by this commit Revision:382855  4.33
pi search for other commits by this committer
biology/seqtools: 4.32 -> 4.33

- Blixem/Dotter
  Multi-dotter support; may now start multiple dotters from blixem
12 Feb 2015 12:04:10
Original commit files touched by this commit Revision:378870  4.32
pi search for other commits by this committer
biology/seqtools: 4.31 -> 4.32

- Blixem
  o Previously-unsupported GFF feature types can now be displayed
    as a new 'basic feature' type.
  o Styles are now applied to the detail view as well as the big
    picture, so feature display is more consistent across the two
    views.
  o Fix a bug where styles were not being applied to
    dynamically-loaded features.
- Dotter
  o Added a 'maximise' button for the greyramp tool.
  o Small fixes to inconsistencies in context-sensitive menus and
    keyboard shortcuts.
13 Dec 2014 18:10:32
Original commit files touched by this commit Revision:374668  4.31
pi search for other commits by this committer
biology/seqtools: 4.30 -> 4.31

Some changes to sqlite dependencies
04 Nov 2014 13:19:24
Original commit files touched by this commit Revision:372142  4.30
pi search for other commits by this committer
biology/seqtools: 4.29 -> 4.30

- Blixem
  o Fix potential crash with internal processing
  o Fix two bugs in data input
15 Oct 2014 18:46:06
Original commit files touched by this commit Revision:370943  4.29
pi search for other commits by this committer
biology/seqtools: 4.28 -> 4.29

- Blixem
  o Added the facility to run Dotter on an ad-hoc sequence (RT:408836).
  o Added the facility to run Dotter against a transcript.
- Dotter
  Minimise the greyramp tool to a simple contrast slider. Use
  Ctrl-G to toggle between this and the full greyramp tool.
- Belvu
  Fix a bug with tree bootstrapping in Belvu.
04 Aug 2014 23:06:21
Original commit files touched by this commit Revision:364067  4.28
bapt search for other commits by this committer
USES=execinfo
31 Jul 2014 03:17:55
Original commit files touched by this commit Revision:363530  4.28
pi search for other commits by this committer
biology/seqtools: 4.27 -> 4.28
15 Jul 2014 23:11:13
Original commit files touched by this commit Revision:362014  4.27
adamw search for other commits by this committer
Add OPTIONS_DEFINE=DOCS for ports with %%PORTDOCS%% in the plist.

Where possible, correct a few instances where PORTDOCS was being used
to flag stuff in EXAMPLESDIR. For some ports, mostly those owned by
ruby@, PORTDOCS is applied to pretty much everything whether it's
documentation or example.
12 Jul 2014 18:56:04
Original commit files touched by this commit Revision:361635  4.27
pi search for other commits by this committer
biology/seqtools: 4.26 -> 4.27
27 Jun 2014 17:21:07
Original commit files touched by this commit Revision:359586  4.26_1
miwi search for other commits by this committer
- Chase database/sqlite3 slib bump

Approved by:	portmgr (myself)
08 Jun 2014 19:51:28
Original commit files touched by this commit Revision:357070  4.26
olgeni search for other commits by this committer
Remove all space characters from Makefile assignments.

No functional changes included.

CR:		D193 (except math/sedumi)
Approved by:	portmgr (bapt)
02 May 2014 19:00:05
Original commit files touched by this commit Revision:352838  4.26
pi search for other commits by this committer
biology/seqtools: 4.25 -> 4.26, fix broken distinfo by upgrading

Submitted by:   pi (myself)
Approved by:    jadawin (mentor)
01 May 2014 16:50:34
Original commit files touched by this commit Revision:352761  4.25
pi search for other commits by this committer
biology/seqtools: 4.24 -> 4.25

PR:             ports/186299
Submitted by:   pi (myself)
Approved by:    jadawin (mentor)
12 Feb 2014 14:03:25
Original commit files touched by this commit Revision:343923  4.24_1
mat search for other commits by this committer
Fix old makeplist bug.

Pointy hat to:	people who blindly use makeplist
Sponsored by:	Absolight
24 Dec 2013 17:23:23
Original commit files touched by this commit Revision:337375  4.24
wg search for other commits by this committer
biology/seqtools: update to 4.24

PR:		ports/185162
Submitted by:	maintainer
14 Nov 2013 20:09:01
Original commit files touched by this commit Revision:333786  4.23
wg search for other commits by this committer
biology/seqtools: update to 4.23

PR:		ports/183960
Submitted by:	maintainer
10 Nov 2013 11:01:03
Original commit files touched by this commit Revision:333374  4.22
wg search for other commits by this committer
biology/seqtools: Tools for visualising sequence alignments

Blixem is an interactive browser of pairwise alignments that have
been stacked up in a "master-slave" multiple alignment; it is not
a 'true' multiple alignment but a 'one-to-many' alignment.

Belvu is a multiple sequence alignment viewer and phylogenetic tool.

Dotter is a graphical dot-matrix program for detailed comparison
of two sequences.

WWW: http://www.sanger.ac.uk/resources/software/seqtools/

PR:		ports/183801
Submitted by:	Kurt Jaeger <fbsd-ports opsec.eu>

Number of commits found: 44