FreshPorts -- The Place For Ports If you buy from Amazon USA, please support us by using this link.
Follow us
Blog
Twitter

non port: head/biology/seqtools/Makefile
SVNWeb

Number of commits found: 30

Fri, 11 Nov 2016
[ 06:19 pi ] Original commit   Revision:425863
425863 biology/seqtools/Makefile
425863 biology/seqtools/distinfo
425863 biology/seqtools/files
425863 biology/seqtools/files/patch-gbtools_src_blatSrc_lib_gff3.c
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.
Sun, 31 Jul 2016
[ 14:19 pi ] Original commit   Revision:419380
419380 biology/seqtools/Makefile
419380 biology/seqtools/distinfo
419380 biology/seqtools/pkg-plist
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
Fri, 22 Apr 2016
[ 16:27 pi ] Original commit   Revision:413787
413787 biology/seqtools/Makefile
413787 biology/seqtools/distinfo
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).
Fri, 1 Apr 2016
[ 13:29 mat ] Original commit   Revision:412344
412344 Mk/Uses/gecko.mk
412344 Mk/bsd.fpc.mk
412344 Mk/bsd.gecko.mk
412344 Mk/bsd.port.mk
412344 accessibility/accerciser/Makefile
412344 accessibility/at-spi/Makefile
412344 accessibility/at-spi2-atk/Makefile
412344 accessibility/at-spi2-core/Makefile
412344 accessibility/caribou/Makefile
412344 accessibility/dasher/Makefile

(Only the first 10 of 1009 ports in this commit are shown above. View all ports for this commit)
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
Mon, 14 Mar 2016
[ 19:40 pi ] Original commit   Revision:411109
411109 biology/seqtools/Makefile
411109 biology/seqtools/distinfo
411109 biology/seqtools/pkg-plist
biology/seqtools: 4.40.0 -> 4.41.1

- mostly internal changes, some build fixes
Sat, 6 Feb 2016
[ 10:17 pi ] Original commit   Revision:408287
408287 biology/seqtools/Makefile
408287 biology/seqtools/distinfo
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.
Sat, 5 Dec 2015
[ 13:20 pi ] Original commit   Revision:403064
403064 biology/seqtools/Makefile
403064 biology/seqtools/distinfo
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.
Tue, 1 Dec 2015
[ 20:50 pi ] Original commit   Revision:402787
402787 biology/seqtools/Makefile
402787 biology/seqtools/distinfo
biology/seqtools: 4.39.1 -> 4.39.2

- Blixem:
  Improve the display of features in the detail view when they
  have transparent fill.
Fri, 13 Nov 2015
[ 18:46 pi ] Original commit   Revision:401527
401527 biology/seqtools/Makefile
401527 biology/seqtools/distinfo
biology/seqtools: 4.39.0 -> 4.39.1

- Fix a bug in Belvu where the display was being initialised in
  command-line-only modes.
Sun, 8 Nov 2015
[ 16:39 pi ] Original commit   Revision:401065
401065 biology/seqtools/Makefile
401065 biology/seqtools/distinfo
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.
Sat, 8 Aug 2015
[ 11:22 pi ] Original commit   Revision:393723
393723 biology/seqtools/Makefile
393723 biology/seqtools/distinfo
biology/seqtools: 4.35 -> 4.36

Minor under-the-hood changes
Tue, 7 Jul 2015
[ 14:17 pi ] Original commit   Revision:391503
391503 biology/seqtools/Makefile
391503 biology/seqtools/distinfo
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)
Wed, 6 May 2015
[ 20:30 pi ] Original commit   Revision:385561
385561 biology/seqtools/Makefile
385561 biology/seqtools/distinfo
385561 biology/seqtools/pkg-plist
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.
Tue, 31 Mar 2015
[ 18:04 pi ] Original commit   Revision:382855
382855 biology/seqtools/Makefile
382855 biology/seqtools/distinfo
biology/seqtools: 4.32 -> 4.33

- Blixem/Dotter
  Multi-dotter support; may now start multiple dotters from blixem
Thu, 12 Feb 2015
[ 12:04 pi ] Original commit   Revision:378870
378870 biology/seqtools/Makefile
378870 biology/seqtools/distinfo
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.
Sat, 13 Dec 2014
[ 18:10 pi ] Original commit   Revision:374668
374668 biology/seqtools/Makefile
374668 biology/seqtools/distinfo
biology/seqtools: 4.30 -> 4.31

Some changes to sqlite dependencies
Tue, 4 Nov 2014
[ 13:19 pi ] Original commit   Revision:372142
372142 biology/seqtools/Makefile
372142 biology/seqtools/distinfo
biology/seqtools: 4.29 -> 4.30

- Blixem
  o Fix potential crash with internal processing
  o Fix two bugs in data input
Wed, 15 Oct 2014
[ 18:46 pi ] Original commit   Revision:370943
370943 biology/seqtools/Makefile
370943 biology/seqtools/distinfo
370943 biology/seqtools/pkg-plist
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.
Mon, 4 Aug 2014
[ 23:06 bapt ] Original commit   Revision:364067
364067 biology/seqtools/Makefile
364067 biology/ugene/Makefile
USES=execinfo
Thu, 31 Jul 2014
[ 03:17 pi ] Original commit   Revision:363530
363530 biology/seqtools/Makefile
363530 biology/seqtools/distinfo
biology/seqtools: 4.27 -> 4.28
Tue, 15 Jul 2014
[ 23:11 adamw ] Original commit   Revision:362014
362014 archivers/bzip2/Makefile
362014 archivers/macutils/Makefile
362014 archivers/ruby-lha/Makefile
362014 archivers/tclmkziplib/Makefile
362014 astro/wcslib/Makefile
362014 audio/abcmidi/Makefile
362014 audio/calf/Makefile
362014 audio/chordpack/Makefile
362014 audio/eawpats/Makefile
362014 audio/espeak/Makefile

(Only the first 10 of 115 ports in this commit are shown above. View all ports for this commit)
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.
Sat, 12 Jul 2014
[ 18:56 pi ] Original commit   Revision:361635
361635 biology/seqtools/Makefile
361635 biology/seqtools/distinfo
biology/seqtools: 4.26 -> 4.27
Fri, 27 Jun 2014
[ 17:21 miwi ] Original commit   Revision:359586
359586 archivers/rpm5/Makefile
359586 astro/osmium/Makefile
359586 audio/firefly/Makefile
359586 audio/gmpc-magnatune/Makefile
359586 audio/gmpc/Makefile
359586 audio/gogglesmm/Makefile
359586 audio/musicpd/Makefile
359586 biology/seqtools/Makefile
359586 chinese/sunpinyin/Makefile
359586 comms/gnokii/Makefile

(Only the first 10 of 94 ports in this commit are shown above. View all ports for this commit)
- Chase database/sqlite3 slib bump

Approved by:	portmgr (myself)
Sun, 8 Jun 2014
[ 19:51 olgeni ] Original commit   Revision:357070
357070 audio/py-pylast/Makefile
357070 audio/sphinxbase/Makefile
357070 biology/seqtools/Makefile
357070 cad/brickutils/Makefile
357070 cad/kicad-devel/Makefile
357070 cad/pcb/Makefile
357070 chinese/msttf/Makefile
357070 converters/asr10/Makefile
357070 converters/bibtexconv/Makefile
357070 databases/luasql-postgres/Makefile

(Only the first 10 of 101 ports in this commit are shown above. View all ports for this commit)
Remove all space characters from Makefile assignments.

No functional changes included.

CR:		D193 (except math/sedumi)
Approved by:	portmgr (bapt)
Fri, 2 May 2014
[ 19:00 pi ] Original commit   Revision:352838
352838 biology/seqtools/Makefile
352838 biology/seqtools/distinfo
biology/seqtools: 4.25 -> 4.26, fix broken distinfo by upgrading

Submitted by:   pi (myself)
Approved by:    jadawin (mentor)
Thu, 1 May 2014
[ 16:50 pi ] Original commit   Revision:352761
352761 biology/seqtools/Makefile
352761 biology/seqtools/distinfo
biology/seqtools: 4.24 -> 4.25

PR:             ports/186299
Submitted by:   pi (myself)
Approved by:    jadawin (mentor)
Wed, 12 Feb 2014
[ 14:03 mat ] Original commit   Revision:343923
343923 biology/seqtools/Makefile
343923 biology/seqtools/pkg-plist
343923 databases/dbtool/Makefile
343923 databases/dbtool/pkg-plist
343923 games/gnubg/Makefile
343923 games/gnubg/pkg-plist
343923 games/pengpong/Makefile
343923 games/pengpong/pkg-plist
343923 games/seabattle/Makefile
343923 games/seabattle/pkg-plist

(Only the first 10 of 20 ports in this commit are shown above. View all ports for this commit)
Fix old makeplist bug.

Pointy hat to:	people who blindly use makeplist
Sponsored by:	Absolight
Tue, 24 Dec 2013
[ 17:23 wg ] Original commit   Revision:337375
337375 biology/seqtools/Makefile
337375 biology/seqtools/distinfo
biology/seqtools: update to 4.24

PR:		ports/185162
Submitted by:	maintainer
Thu, 14 Nov 2013
[ 20:09 wg ] Original commit   Revision:333786
333786 biology/seqtools/Makefile
333786 biology/seqtools/distinfo
biology/seqtools: update to 4.23

PR:		ports/183960
Submitted by:	maintainer
Sun, 10 Nov 2013
[ 11:01 wg ] Original commit   Revision:333374
333374 MOVED
333374 biology/Makefile
333374 biology/dotter
333374 biology/seqtools
333374 biology/seqtools/Makefile
333374 biology/seqtools/distinfo
333374 biology/seqtools/pkg-descr
333374 biology/seqtools/pkg-plist
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: 30

Login
User Login
Create account

Servers and bandwidth provided by
New York Internet, SuperNews, and RootBSD

This site
What is FreshPorts?
About the authors
Issues
FAQ
How big is it?
The latest upgrade!
Privacy
Forums
Blog
Contact

Search
Enter Keywords:
 
more...

Latest Vulnerabilities
firefoxDec 01
firefox-esrDec 01
libxulDec 01
linux-firefoxDec 01
linux-thunderbirdDec 01
thunderbirdDec 01
tsharkDec 01
tshark-liteDec 01
wiresharkDec 01
wireshark-liteDec 01
wireshark-qt5Dec 01
expat2*Nov 30
expat2*Nov 30
gnupg1*Nov 30
libgcrypt*Nov 30

18 vulnerabilities affecting 59 ports have been reported in the past 14 days

* - modified, not new

All vulnerabilities


Ports
Home
Categories
Deleted ports
Sanity Test Failures
Newsfeeds

Statistics
Graphs
NEW Graphs (Javascript)
Traffic

Calculated hourly:
Port count 26920
Broken 314
Deprecated 151
Ignore 577
Forbidden 1
Restricted 213
No CDROM 82
Vulnerable 58
Expired 13
Set to expire 130
Interactive 0
new 24 hours 6
new 48 hours12
new 7 days60
new fortnight106
new month280

Servers and bandwidth provided by
New York Internet, SuperNews, and RootBSD
Valid HTML, CSS, and RSS.
Copyright © 2000-2014 Dan Langille. All rights reserved.