Attachment 62222 Details for Bug 93054 – jalview.shar

jalview.shar

jalview.shar (text/plain), 6.18 KB, created by Fernan Aguero on 2006-02-08 19:20:05 UTC

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Creator: Fernan Aguero

Created: 2006-02-08 19:20:05 UTC

Size: 6.18 KB

patch

obsolete

># 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 <fernan@iib.unsam.edu.ar>
>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 <bsd.port.mk>
>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         </fileset>
>X       </copy>
>X 
>X+
>X       
>X+
>X 	
>X+
>X     </target>
>X     <target name="runenv" depends="init">
>X       <path id="run.classpath">
>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

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Attachments on bug 93054: 62222 | 62223