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>

MOVED

@@ -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

biology/Makefile

@@ -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

biology/dotter/Makefile

@@ -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>

biology/dotter/distinfo

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

biology/dotter/pkg-descr

@@ -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

biology/seqtools/Makefile

@@ -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>

biology/seqtools/distinfo

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

biology/seqtools/pkg-descr

@@ -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/

biology/seqtools/pkg-plist

@@ -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%%