biology/seqtools replaces biology/dotter Fix: #!/bin/sh How-To-Repeat: -
Class Changed From-To: maintainer-update->change-request Fix category (new ports should be change-requests) (via the GNATS Auto Assign Tool)
Responsible Changed From-To: freebsd-ports-bugs->wg wg@ wants this submitter's PRs (via the GNATS Auto Assign Tool)
The attachment did not work well in GNATS, can you attach the shar to me again? Thanks -- William Grzybowski ------------------------------------------ Curitiba/PR - Brasil
Hi! > The attachment did not work well in GNATS, can you attach the shar to me again? Here we go. -- pi@opsec.eu +49 171 3101372 7 years to go !
State Changed From-To: open->closed New port added, with minor changes. Thanks!
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@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> 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 +@dirrmtry %%PORTDOCS%%%%DOCSDIR%% _______________________________________________ svn-ports-all@freebsd.org mailing list http://lists.freebsd.org/mailman/listinfo/svn-ports-all To unsubscribe, send any mail to "svn-ports-all-unsubscribe@freebsd.org"