From owner-freebsd-ports-bugs@FreeBSD.ORG Wed Feb 8 19:20:08 2006 Return-Path: X-Original-To: freebsd-ports-bugs@hub.freebsd.org Delivered-To: freebsd-ports-bugs@hub.freebsd.org Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id 2809716A420 for ; Wed, 8 Feb 2006 19:20:08 +0000 (GMT) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (freefall.freebsd.org [216.136.204.21]) by mx1.FreeBSD.org (Postfix) with ESMTP id 507E443D48 for ; Wed, 8 Feb 2006 19:20:06 +0000 (GMT) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (gnats@localhost [127.0.0.1]) by freefall.freebsd.org (8.13.4/8.13.4) with ESMTP id k18JK66o010391 for ; Wed, 8 Feb 2006 19:20:06 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.13.4/8.13.4/Submit) id k18JK6RP010390; Wed, 8 Feb 2006 19:20:06 GMT (envelope-from gnats) Resent-Date: Wed, 8 Feb 2006 19:20:06 GMT Resent-Message-Id: <200602081920.k18JK6RP010390@freefall.freebsd.org> Resent-From: FreeBSD-gnats-submit@FreeBSD.org (GNATS Filer) Resent-To: freebsd-ports-bugs@FreeBSD.org Resent-Reply-To: FreeBSD-gnats-submit@FreeBSD.org, Fernan Aguero Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id F383816A422 for ; Wed, 8 Feb 2006 19:15:06 +0000 (GMT) (envelope-from fernan@omega.iib.unsam.edu.ar) Received: from omega.iib.unsam.edu.ar (omega.iib.unsam.edu.ar [170.210.49.14]) by mx1.FreeBSD.org (Postfix) with ESMTP id 36A8143D4C for ; Wed, 8 Feb 2006 19:15:04 +0000 (GMT) (envelope-from fernan@omega.iib.unsam.edu.ar) Received: from omega.iib.unsam.edu.ar (localhost [127.0.0.1]) by omega.iib.unsam.edu.ar (8.13.4/8.13.4) with ESMTP id k18JF2RV040983 for ; Wed, 8 Feb 2006 16:15:02 -0300 (ART) (envelope-from fernan@omega.iib.unsam.edu.ar) Received: (from fernan@localhost) by omega.iib.unsam.edu.ar (8.13.4/8.13.3/Submit) id k18JF2LS040982; Wed, 8 Feb 2006 16:15:02 -0300 (ART) (envelope-from fernan) Message-Id: <200602081915.k18JF2LS040982@omega.iib.unsam.edu.ar> Date: Wed, 8 Feb 2006 16:15:02 -0300 (ART) From: Fernan Aguero To: FreeBSD-gnats-submit@FreeBSD.org X-Send-Pr-Version: 3.113 Cc: Subject: ports/93054: [ new port ] biology/jalview X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list Reply-To: Fernan Aguero List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 08 Feb 2006 19:20:08 -0000 X-List-Received-Date: Wed, 08 Feb 2006 19:20:08 -0000 >Number: 93054 >Category: ports >Synopsis: [ new port ] biology/jalview >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Wed Feb 08 19:20:05 GMT 2006 >Closed-Date: >Last-Modified: >Originator: Fernan Aguero >Release: FreeBSD 6.0-RELEASE-p4 i386 >Organization: IIB-UNSAM >Environment: System: FreeBSD omega.iib.unsam.edu.ar 6.0-RELEASE-p4 FreeBSD 6.0-RELEASE-p4 #0: Wed Jan 25 12:43:39 ART 2006 fernan@omega.iib.unsam.edu.ar:/usr/obj/usr/src/sys/OMEGA i386 >Description: A multiple sequence alignment viewer/editor written in Java >How-To-Repeat: >Fix: --- jalview.shar begins here --- # This is a shell archive. Save it in a file, remove anything before # this line, and then unpack it by entering "sh file". Note, it may # create directories; files and directories will be owned by you and # have default permissions. # # This archive contains: # # jalview # jalview/Makefile # jalview/distinfo # jalview/pkg-descr # jalview/pkg-plist # jalview/files # jalview/files/patch-build.xml # jalview/files/jalview.sh.in # echo c - jalview mkdir -p jalview > /dev/null 2>&1 echo x - jalview/Makefile sed 's/^X//' >jalview/Makefile << 'END-of-jalview/Makefile' X# ex:ts=8 X# New ports collection makefile for: jalview X# Date created: 11 Jan 2006 X# Whom: Fernan Aguero X# X# $FreeBSD$ X# X XPORTNAME= jalview XPORTVERSION= 2.07 XCATEGORIES= biology java XMASTER_SITES= http://www.jalview.org/source/ XDISTNAME= ${PORTNAME}_${PORTVERSION:S/./_/} X XMAINTAINER= fernan@iib.unsam.edu.ar XCOMMENT= A viewer and editor for multiple sequence alignments X XUSE_JAVA= yes XJAVA_VERSION= 1.4+ XJAVA_RUN= yes XUSE_ANT= yes XALL_TARGET= makejars XWRKSRC= ${WRKDIR}/${PORTNAME} X XJALVIEW_HOME= ${JAVASHAREDIR}/${PORTNAME} XSUB_FILES= jalview.sh XSUB_LIST= JALVIEW_HOME=${JALVIEW_HOME} X Xdo-install: X ${INSTALL_SCRIPT} ${WRKDIR}/jalview.sh ${PREFIX}/bin/jalview X @${MKDIR} ${JALVIEW_HOME} X ${CP} ${WRKSRC}/dist/* ${JALVIEW_HOME} X X.include END-of-jalview/Makefile echo x - jalview/distinfo sed 's/^X//' >jalview/distinfo << 'END-of-jalview/distinfo' XMD5 (jalview_2_07.tar.gz) = 48261fc1c2dc011fe8788368c8bf8223 XSHA256 (jalview_2_07.tar.gz) = 2cc6b5ec40cf45b0e8e8048b98eacb14af230db6ed6929b95bec4ce0792a51f7 XSIZE (jalview_2_07.tar.gz) = 8439780 END-of-jalview/distinfo echo x - jalview/pkg-descr sed 's/^X//' >jalview/pkg-descr << 'END-of-jalview/pkg-descr' XJalview is a multiple alignment editor written in Java. It is used Xwidely in a variety of web pages (e.g. the EBI Clustalw server and the XPfam protein domain database) but is available as a general purpose Xalignment editor. X Xo Reads and writes alignments in a variety of formats (Fasta, PFAM, MSF, X Clustal, BLC, PIR) Xo Gaps can be inserted/deleted using the mouse. Xo Group editing (insertion deletion of gaps in groups of sequences). Xo Removal of gapped columns. Xo Align sequences using Web Services (Clustal, Muscle...) Xo Amino acid conservation analysis similar to that of AMAS. Xo Alignment sorting options (by name, tree order, percent identity, group). Xo UPGMA and NJ trees calculated and drawn based on percent identity distances. Xo Sequence clustering using principal component analysis. Xo Removal of redundant sequences. Xo Smith Waterman pairwise alignment of selected sequences. Xo Use web based secondary structure prediction programs (JNet). Xo User predefined or custom colour schemes to colour alignments or groups. Xo Sequence feature retrieval and display on the alignment. Xo Print your alignment with colours and annotations. Xo Create HTML pages. Xo Output alignment as portable network graphics image (PNG). Xo Output alignment as encapsulated postscript file (EPS). X XIf you use Jalview in your work, please quote this publication. XClamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), X"The Jalview Java Alignment Editor," Bioinformatics, 12, 426-7 X XWWW: http://www.jalview.org END-of-jalview/pkg-descr echo x - jalview/pkg-plist sed 's/^X//' >jalview/pkg-plist << 'END-of-jalview/pkg-plist' Xbin/jalview Xshare/java/jalview/activation.jar Xshare/java/jalview/xercesImpl.jar Xshare/java/jalview/wsdl4j.jar Xshare/java/jalview/saaj.jar Xshare/java/jalview/regex.jar Xshare/java/jalview/mail.jar Xshare/java/jalview/log4j-1.2.8.jar Xshare/java/jalview/jhall.jar Xshare/java/jalview/jaxrpc.jar Xshare/java/jalview/jalview.jar Xshare/java/jalview/commons-logging.jar Xshare/java/jalview/commons-discovery.jar Xshare/java/jalview/castor-0.9.6-xml.jar Xshare/java/jalview/axis.jar Xshare/java/jalview/xml-apis.jar X@dirrm share/java/jalview X@dirrmtry share/java END-of-jalview/pkg-plist echo c - jalview/files mkdir -p jalview/files > /dev/null 2>&1 echo x - jalview/files/patch-build.xml sed 's/^X//' >jalview/files/patch-build.xml << 'END-of-jalview/files/patch-build.xml' X--- build.xml.orig Mon Dec 12 14:57:02 2005 X+++ build.xml Fri Jan 27 12:20:52 2006 X@@ -180,6 +180,10 @@ X X X X+ X X+ X X+ X X X END-of-jalview/files/patch-build.xml echo x - jalview/files/jalview.sh.in sed 's/^X//' >jalview/files/jalview.sh.in << 'END-of-jalview/files/jalview.sh.in' X#!/bin/sh X# X# $FreeBSD$ X X# Shell script to launch jalview using our javavm wrapper X XJAVA_VERSION=1.4+ %%LOCALBASE%%/bin/java -Djava.ext.dirs=%%JALVIEW_HOME%% -cp %%JALVIEW_HOME%%/jalview.jar jalview.bin.Jalview END-of-jalview/files/jalview.sh.in exit --- jalview.shar ends here --- >Release-Note: >Audit-Trail: >Unformatted: