Date: Fri, 08 Nov 2013 21:31:53 +0100 From: Kurt Jaeger <fbsd-ports@opsec.eu> To: FreeBSD-gnats-submit@freebsd.org Subject: ports/183801: [new port] biology/seqtools, replaces biology/dotter Message-ID: <E1Vesif-0003fU-HZ@f10.opsec.eu> Resent-Message-ID: <201311082040.rA8Ke1qJ064728@freefall.freebsd.org>
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>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@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@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@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@dirrmtry %%PORTDOCS%%%%DOCSDIR%% SHAR_END exit >Release-Note: >Audit-Trail: >Unformatted:
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