Commit graph

39 commits

Author SHA1 Message Date
Kurt Jaeger
397001c1af biology/seqtools: fix build on current, if lld is lld7
- fixed by LLD_UNSAFE=yes

PR:		230609
Submitted by:	jbeich
2019-01-07 19:54:40 +00:00
Gerald Pfeifer
a9f015d155 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
2018-12-12 01:35:33 +00:00
Jan Beich
7067236929 biology/seqtools: re-try on powerpc* after r449590 2017-12-12 03:38:56 +00:00
Mathieu Arnold
3fcd0e41de Remove USES=execinfo.
PR:		220271
Submitted by:	mat (review), Yasuhiro KIMURA (PR)
Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D11488
2017-09-22 10:48:28 +00:00
Gerald Pfeifer
e59c88cece 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
2017-09-10 20:55:38 +00:00
Mark Linimon
fa74598719 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
2017-05-21 21:55:08 +00:00
Gerald Pfeifer
04d6f52202 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
2017-04-01 15:23:30 +00:00
Sunpoet Po-Chuan Hsieh
e0b379fa6f Remove BROKEN_FreeBSD_9
Approved by:	portmgr (blanket)
2017-01-01 03:45:12 +00:00
Kurt Jaeger
8875e10ea5 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.
2016-11-11 06:19:10 +00:00
Kurt Jaeger
02cdc45ea7 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
2016-07-31 14:19:09 +00:00
Kurt Jaeger
4dfa75e3f1 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).
2016-04-22 16:27:25 +00:00
Mathieu Arnold
7f4572eae4 Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
With hat:	portmgr
Sponsored by:	Absolight
2016-04-01 13:29:15 +00:00
Kurt Jaeger
aeb5be07de biology/seqtools: 4.40.0 -> 4.41.1
- mostly internal changes, some build fixes
2016-03-14 19:40:34 +00:00
Kurt Jaeger
0236757375 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.
2016-02-06 10:17:31 +00:00
Kurt Jaeger
2625cb4896 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.
2015-12-05 13:20:21 +00:00
Kurt Jaeger
39967f1619 biology/seqtools: 4.39.1 -> 4.39.2
- Blixem:
  Improve the display of features in the detail view when they
  have transparent fill.
2015-12-01 20:50:34 +00:00
Kurt Jaeger
25eb138c74 biology/seqtools: Fix distinfo, WWW
- Side effect of the seqtools automated build system

Submitted by:	pkg-fallout
2015-11-18 10:53:48 +00:00
Kurt Jaeger
ccc48e7454 biology/seqtools: 4.39.0 -> 4.39.1
- Fix a bug in Belvu where the display was being initialised in
  command-line-only modes.
2015-11-13 18:46:02 +00:00
Kurt Jaeger
d2b692548d 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.
2015-11-08 16:39:58 +00:00
Kurt Jaeger
0269d640fc biology/seqtools: 4.35 -> 4.36
Minor under-the-hood changes
2015-08-08 11:22:24 +00:00
Kurt Jaeger
97a21e2f53 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)
2015-07-07 14:17:51 +00:00
Kurt Jaeger
681df24d3b 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.
2015-05-06 20:30:53 +00:00
Kurt Jaeger
fd18692b42 biology/seqtools: 4.32 -> 4.33
- Blixem/Dotter
  Multi-dotter support; may now start multiple dotters from blixem
2015-03-31 18:04:25 +00:00
Kurt Jaeger
507078b95f 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.
2015-02-12 12:04:09 +00:00
Kurt Jaeger
c66ecfff29 biology/seqtools: 4.30 -> 4.31
Some changes to sqlite dependencies
2014-12-13 18:10:31 +00:00
Kurt Jaeger
0c6932686b biology/seqtools: 4.29 -> 4.30
- Blixem
  o Fix potential crash with internal processing
  o Fix two bugs in data input
2014-11-04 13:19:23 +00:00
Kurt Jaeger
cb7f36c606 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.
2014-10-15 18:46:05 +00:00
Baptiste Daroussin
895c00dee5 USES=execinfo 2014-08-04 23:06:21 +00:00
Kurt Jaeger
ee152dadd7 biology/seqtools: 4.27 -> 4.28 2014-07-31 03:17:54 +00:00
Adam Weinberger
44eaadcb75 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.
2014-07-15 23:11:12 +00:00
Kurt Jaeger
c633e61a10 biology/seqtools: 4.26 -> 4.27 2014-07-12 18:56:03 +00:00
Martin Wilke
bd48d39657 - Chase database/sqlite3 slib bump
Approved by:	portmgr (myself)
2014-06-27 17:21:06 +00:00
Jimmy Olgeni
55dc0f983a Remove all space characters from Makefile assignments.
No functional changes included.

CR:		D193 (except math/sedumi)
Approved by:	portmgr (bapt)
2014-06-08 19:51:27 +00:00
Kurt Jaeger
07685f17fd biology/seqtools: 4.25 -> 4.26, fix broken distinfo by upgrading
Submitted by:   pi (myself)
Approved by:    jadawin (mentor)
2014-05-02 19:00:04 +00:00
Kurt Jaeger
4e90cff927 biology/seqtools: 4.24 -> 4.25
PR:             ports/186299
Submitted by:   pi (myself)
Approved by:    jadawin (mentor)
2014-05-01 16:50:34 +00:00
Mathieu Arnold
33ab73cd19 Fix old makeplist bug.
Pointy hat to:	people who blindly use makeplist
Sponsored by:	Absolight
2014-02-12 14:03:25 +00:00
William Grzybowski
1f6544c522 biology/seqtools: update to 4.24
PR:		ports/185162
Submitted by:	maintainer
2013-12-24 17:23:23 +00:00
William Grzybowski
75a509365b biology/seqtools: update to 4.23
PR:		ports/183960
Submitted by:	maintainer
2013-11-14 20:09:00 +00:00
William Grzybowski
20139c3cfa 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>
2013-11-10 11:01:02 +00:00