svn commit: r333374 - in head: . biology biology/dotter biology/seqtools

[William Grzybowski]

Author: wg
Date: Sun Nov 10 11:01:02 2013
New Revision: 333374
URL: http://svnweb.freebsd.org/changeset/ports/333374

Log:
  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>

Added:
  head/biology/seqtools/
  head/biology/seqtools/Makefile   (contents, props changed)
  head/biology/seqtools/distinfo   (contents, props changed)
  head/biology/seqtools/pkg-descr   (contents, props changed)
  head/biology/seqtools/pkg-plist   (contents, props changed)
Deleted:
  head/biology/dotter/
Modified:
  head/MOVED
  head/biology/Makefile

Modified: head/MOVED
==============================================================================
--- head/MOVED	Sun Nov 10 10:59:22 2013	(r333373)
+++ head/MOVED	Sun Nov 10 11:01:02 2013	(r333374)
@@ -5177,3 +5177,4 @@ devel/pure-stlvec|devel/pure-stllib|2013
 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

Modified: head/biology/Makefile
==============================================================================
--- head/biology/Makefile	Sun Nov 10 10:59:22 2013	(r333373)
+++ head/biology/Makefile	Sun Nov 10 11:01:02 2013	(r333374)
@@ -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

Added: head/biology/seqtools/Makefile
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/seqtools/Makefile	Sun Nov 10 11:01:02 2013	(r333374)
@@ -0,0 +1,25 @@
+# Created by: Kurt Jaeger <fbsd-ports at 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 at 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>

Added: head/biology/seqtools/distinfo
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/seqtools/distinfo	Sun Nov 10 11:01:02 2013	(r333374)
@@ -0,0 +1,2 @@
+SHA256 (seqtools-4.22.tar.gz) = c0e782e7b5f705056a91c038684bde41833aba89bd7b4ba8531c15bb6ebf5ea8
+SIZE (seqtools-4.22.tar.gz) = 7049945

Added: head/biology/seqtools/pkg-descr
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/seqtools/pkg-descr	Sun Nov 10 11:01:02 2013	(r333374)
@@ -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/

Added: head/biology/seqtools/pkg-plist
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/seqtools/pkg-plist	Sun Nov 10 11:01:02 2013	(r333374)
@@ -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
+ at dirrmtry %%PORTDOCS%%%%DOCSDIR%%