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Port details
seqtools Tools for visualising sequence alignments
4.44.1 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
Maintainer: pi@FreeBSD.org search for ports maintained by this maintainer
Port Added: 10 Nov 2013 11:01:14
License: GPLv3
A suite of 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.
It has an extensive set of user-configurable modes to color residues
by conservation or by residue type, and some basic alignment editing
capabilities.

Dotter is a graphical dot-matrix program for detailed comparison
of two sequences. Every residue in one sequence is compared to every
residue in the other, with one sequence plotted on the x-axis and
the other on the y-axis.

WWW: http://www.sanger.ac.uk/science/tools/seqtools
SVNWeb : Homepage : PortsMon

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

PKGNAME: seqtools

distinfo:

TIMESTAMP = 1478810582
SHA256 (seqtools-4.44.1.tar.gz) = 0e1dd7087d1180e434f0ea1aac21b8dfb5261195581ec3ba012abf0d1e39daa9
SIZE (seqtools-4.44.1.tar.gz) = 6922888


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

Build dependencies:
  1. msgfmt : devel/gettext-tools
  2. pkgconf>=0.9.10 : devel/pkgconf
  3. 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. libgtk-x11-2.0.so : x11-toolkits/gtk20
  11. libpango-1.0.so : x11-toolkits/pango
There are no ports dependent upon this port

Configuration Options
===> The following configuration options are available for seqtools-4.44.1:
     DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings

USES:
compiler:c++14-lang execinfo gettext libtool pkgconfig gnome

Master Sites:
  1. ftp://ftp.sanger.ac.uk/pub4/resources/software/seqtools/PRODUCTION/
Port Moves
  • port moved here from biology/dotter on 2013-11-10
    REASON: Replaced with biology/seqtools

Number of commits found: 31

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
11 Nov 2016 06:19:10
Original commit files touched by this commit  4.44.1
Revision:425863
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  4.43.0
Revision:419380
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  4.42.1
Revision:413787
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  4.41.1
Revision:412344
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  4.41.1
Revision:411109
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  4.40.0
Revision:408287
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  4.39.3
Revision:403064
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  4.39.2
Revision:402787
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  4.39.1
Revision:401862
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  4.39.1
Revision:401527
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  4.39.0
Revision:401065
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  4.36
Revision:393723
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  4.35
Revision:391503
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  4.34.1
Revision:385561
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  4.33
Revision:382855
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  4.32
Revision:378870
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  4.31
Revision:374668
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  4.30
Revision:372142
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  4.29
Revision:370943
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  4.28
Revision:364067
bapt search for other commits by this committer
USES=execinfo
31 Jul 2014 03:17:55
Original commit files touched by this commit  4.28
Revision:363530
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  4.27
Revision:362014
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  4.27
Revision:361635
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  4.26_1
Revision:359586
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  4.26
Revision:357070
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  4.26
Revision:352838
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  4.25
Revision:352761
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  4.24_1
Revision:343923
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  4.24
Revision:337375
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  4.23
Revision:333786
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  4.22
Revision:333374
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: 31

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