| non port: biology/seqtools/Makefile |
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SVNWeb
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Number of commits found: 42 |
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Sat, 4 Apr 2020
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[ 20:51 antoine  ]   (Only the first 10 of 520 ports in this commit are shown above.  )
Deprecate ports broken for more than 6 months
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Wed, 6 Nov 2019
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[ 12:48 antoine ] (Only the first 10 of 268 ports in this commit are shown above. )
Mark a few ports BROKEN, unfetchable
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Mon, 4 Nov 2019
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[ 21:08 zeising ] (Only the first 10 of 11 ports in this commit are shown above. )
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'.
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Fri, 26 Jul 2019
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[ 20:46 gerald ] (Only the first 10 of 3853 ports in this commit are shown above. )
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
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Mon, 7 Jan 2019
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[ 19:54 pi ]
biology/seqtools: fix build on current, if lld is lld7
- fixed by LLD_UNSAFE=yes
PR: 230609
Submitted by: jbeich
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Wed, 12 Dec 2018
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[ 01:35 gerald ] (Only the first 10 of 3168 ports in this commit are shown above. )
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
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Tue, 12 Dec 2017
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[ 03:38 jbeich ]
biology/seqtools: re-try on powerpc* after r449590
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Fri, 22 Sep 2017
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[ 10:48 mat ] (Only the first 10 of 175 ports in this commit are shown above. )
Remove USES=execinfo.
PR: 220271
Submitted by: mat (review), Yasuhiro KIMURA (PR)
Sponsored by: Absolight
Differential Revision: https://reviews.freebsd.org/D11488
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Sun, 10 Sep 2017
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[ 20:55 gerald ] (Only the first 10 of 1201 ports in this commit are shown above. )
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
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Sun, 21 May 2017
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[ 21:55 linimon ] (Only the first 10 of 49 ports in this commit are shown above. )
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
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Sat, 1 Apr 2017
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[ 15:23 gerald ] (Only the first 10 of 1118 ports in this commit are shown above. )
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
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Sun, 1 Jan 2017
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[ 03:45 sunpoet ] (Only the first 10 of 161 ports in this commit are shown above. )
Remove BROKEN_FreeBSD_9
Approved by: portmgr (blanket)
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Fri, 11 Nov 2016
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[ 06:19 pi ]
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.
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Sun, 31 Jul 2016
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[ 14:19 pi ]
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
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Fri, 22 Apr 2016
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[ 16:27 pi ]
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).
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Fri, 1 Apr 2016
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[ 13:29 mat ] (Only the first 10 of 1009 ports in this commit are shown above. )
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
With hat: portmgr
Sponsored by: Absolight
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Mon, 14 Mar 2016
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[ 19:40 pi ]
biology/seqtools: 4.40.0 -> 4.41.1
- mostly internal changes, some build fixes
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Sat, 6 Feb 2016
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[ 10:17 pi ]
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.
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Sat, 5 Dec 2015
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[ 13:20 pi ]
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.
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Tue, 1 Dec 2015
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[ 20:50 pi ]
biology/seqtools: 4.39.1 -> 4.39.2
- Blixem:
Improve the display of features in the detail view when they
have transparent fill.
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Fri, 13 Nov 2015
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[ 18:46 pi ]
biology/seqtools: 4.39.0 -> 4.39.1
- Fix a bug in Belvu where the display was being initialised in
command-line-only modes.
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Sun, 8 Nov 2015
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[ 16:39 pi ]
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.
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Sat, 8 Aug 2015
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[ 11:22 pi ]
biology/seqtools: 4.35 -> 4.36
Minor under-the-hood changes
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Tue, 7 Jul 2015
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[ 14:17 pi ]
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)
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Wed, 6 May 2015
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[ 20:30 pi ]
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.
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Tue, 31 Mar 2015
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[ 18:04 pi ]
biology/seqtools: 4.32 -> 4.33
- Blixem/Dotter
Multi-dotter support; may now start multiple dotters from blixem
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Thu, 12 Feb 2015
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[ 12:04 pi ]
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.
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Sat, 13 Dec 2014
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[ 18:10 pi ]
biology/seqtools: 4.30 -> 4.31
Some changes to sqlite dependencies
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Tue, 4 Nov 2014
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[ 13:19 pi ]
biology/seqtools: 4.29 -> 4.30
- Blixem
o Fix potential crash with internal processing
o Fix two bugs in data input
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Wed, 15 Oct 2014
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[ 18:46 pi ]
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.
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Mon, 4 Aug 2014
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[ 23:06 bapt ]
USES=execinfo
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Thu, 31 Jul 2014
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[ 03:17 pi ]
biology/seqtools: 4.27 -> 4.28
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Tue, 15 Jul 2014
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[ 23:11 adamw ] (Only the first 10 of 115 ports in this commit are shown above. )
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.
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Sat, 12 Jul 2014
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[ 18:56 pi ]
biology/seqtools: 4.26 -> 4.27
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Fri, 27 Jun 2014
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[ 17:21 miwi ] (Only the first 10 of 94 ports in this commit are shown above. )
- Chase database/sqlite3 slib bump
Approved by: portmgr (myself)
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Sun, 8 Jun 2014
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[ 19:51 olgeni ] (Only the first 10 of 101 ports in this commit are shown above. )
Remove all space characters from Makefile assignments.
No functional changes included.
CR: D193 (except math/sedumi)
Approved by: portmgr (bapt)
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Fri, 2 May 2014
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[ 19:00 pi ]
biology/seqtools: 4.25 -> 4.26, fix broken distinfo by upgrading
Submitted by: pi (myself)
Approved by: jadawin (mentor)
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Thu, 1 May 2014
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[ 16:50 pi ]
biology/seqtools: 4.24 -> 4.25
PR: ports/186299
Submitted by: pi (myself)
Approved by: jadawin (mentor)
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Wed, 12 Feb 2014
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[ 14:03 mat ] (Only the first 10 of 20 ports in this commit are shown above. )
Fix old makeplist bug.
Pointy hat to: people who blindly use makeplist
Sponsored by: Absolight
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Tue, 24 Dec 2013
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[ 17:23 wg ]
biology/seqtools: update to 4.24
PR: ports/185162
Submitted by: maintainer
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Thu, 14 Nov 2013
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[ 20:09 wg ]
biology/seqtools: update to 4.23
PR: ports/183960
Submitted by: maintainer
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Sun, 10 Nov 2013
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[ 11:01 wg ]
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>
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Number of commits found: 42 |
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