ports/183801: [new port] biology/seqtools, replaces biology/dotter

[Kurt Jaeger]

>Number:         183801
>Category:       ports
>Synopsis:       [new port] biology/seqtools, replaces biology/dotter
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          maintainer-update
>Submitter-Id:   current-users
>Arrival-Date:   Fri Nov 08 20:40:01 UTC 2013
>Closed-Date:
>Last-Modified:
>Originator:     Kurt Jaeger
>Release:        FreeBSD 10.0-BETA3 amd64
>Organization:
-
>Environment:
System: FreeBSD f10.opsec.eu 10.0-BETA3 FreeBSD 10.0-BETA3 #0 r257580: Sun Nov  3 19:43:01 UTC 2013     root at snap.freebsd.org:/usr/obj/usr/src/sys/GENERIC  amd64

>Description:
	biology/seqtools replaces biology/dotter

>How-To-Repeat:
	-
>Fix:

#!/bin/sh
# This is a shell archive
echo x biology/seqtools
mkdir -p biology/seqtools > /dev/null 2>&1
echo x biology/seqtools/pkg-descr
sed 's/^X//' > biology/seqtools/pkg-descr << 'SHAR_END'
XA suite of tools for visualising sequence alignments.
X
XBlixem is an interactive browser of pairwise alignments that have
Xbeen stacked up in a "master-slave" multiple alignment; it is not
Xa 'true' multiple alignment but a 'one-to-many' alignment. It
Xdisplays an overview section showing the positions of genes and
Xalignments around the alignment window, and a detail section showing
Xthe actual alignment of protein or nucleotide sequences to the
Xgenomic DNA sequence.
X
XBelvu is a multiple sequence alignment viewer and phylogenetic tool.
XIt has an extensive set of user-configurable modes to color residues
Xby conservation or by residue type, and some basic alignment editing
Xcapabilities. It can generate distance matrices between sequences
Xand construct distance-based trees, either graphically or as part
Xof a phylogenetic software pipeline.
X
XDotter is a graphical dot-matrix program for detailed comparison
Xof two sequences. Every residue in one sequence is compared to every
Xresidue in the other, with one sequence plotted on the x-axis and
Xthe other on the y-axis. Noise is filtered out so that alignments
Xappear as diagonal lines.
X
XDotter provides a tool to explore the visual appearance of this
Xlandscape, as well as a tool to examine the sequence alignment it
Xrepresents.
X
XWWW: http://www.sanger.ac.uk/resources/software/seqtools/
SHAR_END
echo x biology/seqtools/Makefile
sed 's/^X//' > biology/seqtools/Makefile << 'SHAR_END'
X# Created by: Kurt Jaeger <fbsd-ports at opsec.eu>
X# $FreeBSD$
X
XPORTNAME=	seqtools
XPORTVERSION=	4.22
XCATEGORIES=	biology
XMASTER_SITES=	ftp://ftp.sanger.ac.uk/pub4/resources/software/seqtools/PRODUCTION/
X
XMAINTAINER=	fbsd-ports at opsec.eu
XCOMMENT=	Tools for visualising sequence alignments
X
XLICENSE=        GPLv3
X
XGNU_CONFIGURE=	yes
XUSE_GCC=	any
XUSE_GNOME=	gtk20
XLDFLAGS+=	-lexecinfo -lcurl -lm
XMAKE_JOBS_UNSAFE=	yes
X
X.include <bsd.port.mk>
SHAR_END
echo x biology/seqtools/distinfo
sed 's/^X//' > biology/seqtools/distinfo << 'SHAR_END'
XSHA256 (seqtools-4.22.tar.gz) = c0e782e7b5f705056a91c038684bde41833aba89bd7b4ba8531c15bb6ebf5ea8
XSIZE (seqtools-4.22.tar.gz) = 7049945
SHAR_END
echo x biology/seqtools/pkg-plist
sed 's/^X//' > biology/seqtools/pkg-plist << 'SHAR_END'
Xbin/belvu
Xbin/blixem
Xbin/blixemh
Xbin/dotter
X%%PORTDOCS%%%%DOCSDIR%%/Belvu_manual.pdf
X%%PORTDOCS%%%%DOCSDIR%%/Blixem_manual.pdf
X%%PORTDOCS%%%%DOCSDIR%%/Dotter_manual.pdf
X%%PORTDOCS%%%%DOCSDIR%%/belvu_quick_start.html
X%%PORTDOCS%%%%DOCSDIR%%/belvu_usage.txt
X%%PORTDOCS%%%%DOCSDIR%%/blixem_quick_start.html
X%%PORTDOCS%%%%DOCSDIR%%/blixem_usage.txt
X%%PORTDOCS%%%%DOCSDIR%%/dotter_quick_start.html
X%%PORTDOCS%%%%DOCSDIR%%/dotter_usage.txt
X%%PORTDOCS%%%%DOCSDIR%%/release_notes.html
X%%PORTDOCS%%%%DOCSDIR%%/todo.html
X at dirrmtry %%PORTDOCS%%%%DOCSDIR%%
SHAR_END
exit
>Release-Note:
>Audit-Trail:
>Unformatted: