sync/ports
1
0
Fork 0
mirror of https://git.freebsd.org/ports.git synced 2025-06-01 02:46:27 -04:00
Code Issues Projects Releases Packages Wiki Activity Actions

biology/seqtools: Tools for visualising sequence alignments

Browse source 
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>
This commit is contained in:
William Grzybowski 2013-11-10 11:01:02 +00:00
parent 8f33e80ccd
commit 20139c3cfa
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=333374
9 changed files with 62 additions and 60 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

1
MOVED
View file

@ -5177,3 +5177,4 @@ devel/pure-stlvec|devel/pure-stllib|2013-11-07|Removed: Use devel/pure-stllib in
textproc/lexxia||2013-11-07|Removed no public distfile available anymore
textproc/docproj-nojadetex||2013-11-07|Removed
games/frozenbubble|games/frozen-bubble|2013-11-08|Renamed to match upstream naming
biology/dotter|biology/seqtools|2013-11-10|Replaced with biology/seqtools

2
biology/Makefile
View file

@ -16,7 +16,6 @@
SUBDIR += clustalw
SUBDIR += consed
SUBDIR += crux
SUBDIR += dotter
SUBDIR += embassy
SUBDIR += emboss
SUBDIR += fasta
@ -86,6 +85,7 @@
SUBDIR += seaview
SUBDIR += seqan
SUBDIR += seqio
SUBDIR += seqtools
SUBDIR += sim4
SUBDIR += ssaha
SUBDIR += tRNAscan-SE

35
biology/dotter/Makefile
View file

@ -1,35 +0,0 @@
# Created by: Fernan Aguero <fernan@iib.unsam.edu.ar>
# $FreeBSD$
PORTNAME= dotter
PORTVERSION= 20021204 # last modified date in FTP server
CATEGORIES= biology
MASTER_SITES= http://sonnhammer.sbc.su.se/download/software/dotter/ \
LOCAL/glarkin
DISTNAME= ${PORTNAME}.LIN
EXTRACT_SUFX= #
DIST_SUBDIR= ${PORTNAME}-${PORTVERSION}
EXTRACT_ONLY= #
MAINTAINER= fbsd-ports@opsec.eu
COMMENT= Viewer for multiple sequence alignments
DEPRECATED= Broken for more than 6 month
EXPIRATION_DATE= 2013-12-18
BROKEN= checksum mismatch
USE_LINUX= yes
ONLY_FOR_ARCHS= i386
NO_BUILD= yes
PLIST_FILES= bin/${PORTNAME} bin/${DISTNAME}
NO_STAGE= yes
do-install:
${BRANDELF} -t Linux ${DISTDIR}/${DIST_SUBDIR}/${DISTNAME}
${INSTALL_PROGRAM} ${DISTDIR}/${DIST_SUBDIR}/${DISTNAME} \
${PREFIX}/bin
( cd ${PREFIX}/bin && ${LN} -s ${DISTNAME} ${PORTNAME} )
.include <bsd.port.mk>

2
biology/dotter/distinfo
View file

@ -1,2 +0,0 @@
SHA256 (dotter-20021204/dotter.LIN) = c66bae7704b2fa305f848451cf35b7a0738a3fd57468da1393684328f111cd75
SIZE (dotter-20021204/dotter.LIN) = 4804333

22
biology/dotter/pkg-descr
View file

@ -1,22 +0,0 @@
Dotter is a graphical dotplot program for detailed comparison of
two sequences. Here, every residue in one sequence is compared to
every residue in the other sequence. The first sequence runs along
the x-axis and the second sequence along the y-axis. In regions
where the two sequences are similar to each other, a row of high
scores will run diagonally across the dot matrix. If you're comparing
a sequence against itself to find internal repeats, you'll notice
that the main diagonal scores maximally, since it's the 100% perfect
self-match.
To make the score matrix more intelligible, the pairwise scores are
averaged over a sliding window which runs diagonally. The averaged
score matrix forms a three-dimensional landscape, with the two
sequences in two dimensions and the height of the peaks in the
third. This landscape is projected onto two dimensions by aid of
greyscales - the darker grey of a peak, the higher it is.
Dotter provides a tool to explore the visual appearance of this
landscape, as well as a tool to examine the sequence alignment it
represents.
WWW: http://sonnhammer.sbc.su.se/Dotter.html

25
biology/seqtools/Makefile Normal file
View file

@ -0,0 +1,25 @@
# Created by: Kurt Jaeger <fbsd-ports@opsec.eu>
# $FreeBSD$
PORTNAME= seqtools
PORTVERSION= 4.22
CATEGORIES= biology
MASTER_SITES= ftp://ftp.sanger.ac.uk/pub4/resources/software/seqtools/PRODUCTION/
MAINTAINER= fbsd-ports@opsec.eu
COMMENT= Tools for visualising sequence alignments
LICENSE= GPLv3
LIB_DEPENDS= libcurl.so:${PORTSDIR}/ftp/curl \
libexecinfo.so:${PORTSDIR}/devel/libexecinfo \
USES= pkgconfig
GNU_CONFIGURE= yes
USE_GCC= any
USE_GNOME= gtk20
CFLAGS= -I${LOCALBASE}/include
LDFLAGS= -L${LOCALBASE}/lib -lexecinfo -lcurl
MAKE_JOBS_UNSAFE= yes
.include <bsd.port.mk>

2
biology/seqtools/distinfo Normal file
View file

@ -0,0 +1,2 @@
SHA256 (seqtools-4.22.tar.gz) = c0e782e7b5f705056a91c038684bde41833aba89bd7b4ba8531c15bb6ebf5ea8
SIZE (seqtools-4.22.tar.gz) = 7049945

17
biology/seqtools/pkg-descr Normal file
View file

@ -0,0 +1,17 @@
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/resources/software/seqtools/

16
biology/seqtools/pkg-plist Normal file
View file

@ -0,0 +1,16 @@
bin/belvu
bin/blixem
bin/blixemh
bin/dotter
%%PORTDOCS%%%%DOCSDIR%%/Belvu_manual.pdf
%%PORTDOCS%%%%DOCSDIR%%/Blixem_manual.pdf
%%PORTDOCS%%%%DOCSDIR%%/Dotter_manual.pdf
%%PORTDOCS%%%%DOCSDIR%%/belvu_quick_start.html
%%PORTDOCS%%%%DOCSDIR%%/belvu_usage.txt
%%PORTDOCS%%%%DOCSDIR%%/blixem_quick_start.html
%%PORTDOCS%%%%DOCSDIR%%/blixem_usage.txt
%%PORTDOCS%%%%DOCSDIR%%/dotter_quick_start.html
%%PORTDOCS%%%%DOCSDIR%%/dotter_usage.txt
%%PORTDOCS%%%%DOCSDIR%%/release_notes.html
%%PORTDOCS%%%%DOCSDIR%%/todo.html
@dirrmtry %%PORTDOCS%%%%DOCSDIR%%