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Date: Wed, 8 Feb 2006 16:15:02 -0300 (ART)
From: Fernan Aguero <fernan@iib.unsam.edu.ar>
Reply-To: Fernan Aguero <fernan@iib.unsam.edu.ar>
To: FreeBSD-gnats-submit@freebsd.org
Cc:
Subject: [ new port ] biology/jalview
X-Send-Pr-Version: 3.113
X-GNATS-Notify:

>Number:         93054
>Category:       ports
>Synopsis:       [ new port ] biology/jalview
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    hq
>State:          closed
>Quarter:        
>Keywords:       
>Date-Required:  
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Wed Feb 08 19:20:05 GMT 2006
>Closed-Date:    Mon Feb 13 09:44:05 GMT 2006
>Last-Modified:  Mon Feb 13 09:44:05 GMT 2006
>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 <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 <!-- the default keystore details might need to be edited here -->
X+<!-- Remove all the remaining stuff for this target 
X+     which is only necessary if we want to start jalview
X+     using java web start. It requires us to generate a key 
X+     before building the port - Fernan - 27.Jan.2006 
X       <signjar
X       storepass="alignmentisfun"
X       keypass="alignmentisfun"
X@@ -194,8 +198,9 @@
X       </fileset>
X       </signjar>
X       <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties"/>
X-
X+-->
X       <!--    codebase="http://www.jalview.org/jalview/webstart" -->
X+<!--
X       <jnlp toFile="${packageDir}/jalview.jnlp" href="jalview.jnlp"
X       codebase="${WebStartLocation}">
X       <information>
X@@ -206,6 +211,7 @@
X         <description kind="short">Jalview</description>
X         <icon href="logo_big.gif"/>
X         <offline_allowed/>
X+-->
X 	<!--
X 	<association mime-type="application-x/ext-file" extensions="fa"/>
X         <association mime-type="application-x/ext-file" extensions="fasta"/>
X@@ -216,6 +222,7 @@
X         <association mime-type="application-x/ext-file" extensions="aln"/>
X         <association mime-type="application-x/ext-file" extensions="pir"/>
X 	-->
X+<!--
X        </information>
X         <resources>
X           <j2se version="1.4+"/>
X@@ -234,6 +241,7 @@
X           <all_permissions/>
X         </security>
X       </jnlp>
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
--- jalview.shar ends here ---

>Release-Note:
>Audit-Trail:
Responsible-Changed-From-To: freebsd-ports-bugs->hq 
Responsible-Changed-By: hq 
Responsible-Changed-When: Fri Feb 10 10:26:17 UTC 2006 
Responsible-Changed-Why:  
I'll handle this. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=93054 

From: Herve Quiroz <herve.quiroz@esil.univ-mrs.fr>
To: bug-followup@FreeBSD.org, fernan@iib.unsam.edu.ar
Cc:  
Subject: Re: ports/93054: [ new port ] biology/jalview
Date: Fri, 10 Feb 2006 11:36:32 +0100

 Hi,
 
 The port needs to be improved before we add it to the tree. Here is a
 new version:
 
 - Don't set JAVA_RUN
 - Use DATADIR instead of JALVIEW_HOME (and it's already included in
   SUB_LIST)
 - Use %%DATADIR%% in pkg-plist
 - Use %%JAVA_VERSION%% in the launcher shell script (in case the user
   wants to override JAVA_VERSION whe building the port)
 - Comment the patch
 - Add a $FreeBSD$ tag in pkg-plist and the patch file
 - Makefile should not contain editor hints (ex:ts=8)
 - Use INSTALL_DATA rather than CP when installing JAR files
 
 There is one more issue I could not handle: portlint reports that the
 pkg-descr in too long (30 lines when the maximum length is 24 lines).
 
 Could you please review the new version and fix pkg-descr?
 
 Herve
 
 
 # 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# 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+
 XUSE_ANT=	yes
 XALL_TARGET=	makejars
 XWRKSRC=		${WRKDIR}/${PORTNAME}
 X
 XDATADIR=	${JAVASHAREDIR}/${PORTNAME}
 XSUB_FILES=	jalview.sh
 X
 Xdo-install:
 X	${INSTALL_SCRIPT} ${WRKDIR}/jalview.sh ${PREFIX}/bin/jalview
 X	@${MKDIR} ${DATADIR}
 X	${INSTALL_DATA} ${WRKSRC}/dist/* ${DATADIR}
 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'
 X@comment $FreeBSD$
 Xbin/jalview
 X%%DATADIR%%/activation.jar
 X%%DATADIR%%/xercesImpl.jar
 X%%DATADIR%%/wsdl4j.jar
 X%%DATADIR%%/saaj.jar
 X%%DATADIR%%/regex.jar
 X%%DATADIR%%/mail.jar
 X%%DATADIR%%/log4j-1.2.8.jar
 X%%DATADIR%%/jhall.jar
 X%%DATADIR%%/jaxrpc.jar
 X%%DATADIR%%/jalview.jar
 X%%DATADIR%%/commons-logging.jar
 X%%DATADIR%%/commons-discovery.jar
 X%%DATADIR%%/castor-0.9.6-xml.jar
 X%%DATADIR%%/axis.jar
 X%%DATADIR%%/xml-apis.jar
 X@dirrm %%DATADIR%%
 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$FreeBSD$
 X
 XThis patch removes the webstart support.
 X
 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 <!-- the default keystore details might need to be edited here -->
 X+<!-- Remove all the remaining stuff for this target 
 X+     which is only necessary if we want to start jalview
 X+     using java web start. It requires us to generate a key 
 X+     before building the port - Fernan - 27.Jan.2006 
 X       <signjar
 X       storepass="alignmentisfun"
 X       keypass="alignmentisfun"
 X@@ -194,8 +198,9 @@
 X       </fileset>
 X       </signjar>
 X       <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties"/>
 X-
 X+-->
 X       <!--    codebase="http://www.jalview.org/jalview/webstart" -->
 X+<!--
 X       <jnlp toFile="${packageDir}/jalview.jnlp" href="jalview.jnlp"
 X       codebase="${WebStartLocation}">
 X       <information>
 X@@ -206,6 +211,7 @@
 X         <description kind="short">Jalview</description>
 X         <icon href="logo_big.gif"/>
 X         <offline_allowed/>
 X+-->
 X 	<!--
 X 	<association mime-type="application-x/ext-file" extensions="fa"/>
 X         <association mime-type="application-x/ext-file" extensions="fasta"/>
 X@@ -216,6 +222,7 @@
 X         <association mime-type="application-x/ext-file" extensions="aln"/>
 X         <association mime-type="application-x/ext-file" extensions="pir"/>
 X 	-->
 X+<!--
 X        </information>
 X         <resources>
 X           <j2se version="1.4+"/>
 X@@ -234,6 +241,7 @@
 X           <all_permissions/>
 X         </security>
 X       </jnlp>
 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="%%JAVA_VERSION%%" "%%LOCALBASE%%/bin/java" -Djava.ext.dirs="%%DATADIR%%" -cp "%%DATADIR%%/jalview.jar" jalview.bin.Jalview
 END-of-jalview/files/jalview.sh.in
 exit
 
State-Changed-From-To: open->feedback 
State-Changed-By: hq 
State-Changed-When: Fri Feb 10 10:40:59 UTC 2006 
State-Changed-Why:  
Submitter asked for a review. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=93054 

From: Fernan Aguero <fernan@iib.unsam.edu.ar>
To: Herve Quiroz <herve.quiroz@esil.univ-mrs.fr>
Cc: bug-followup@freebsd.org
Subject: Re: ports/93054: [ new port ] biology/jalview
Date: Fri, 10 Feb 2006 16:17:39 -0300

 --yrj/dFKFPuw6o+aM
 Content-Type: text/plain; charset=us-ascii
 Content-Disposition: inline
 
 +----[ Herve Quiroz <herve.quiroz@esil.univ-mrs.fr> (10.Feb.2006 14:57):
 |
 | Hi,
 | 
 | The port needs to be improved before we add it to the tree. Here is a
 | new version:
 | 
 | - Don't set JAVA_RUN
 | - Use DATADIR instead of JALVIEW_HOME (and it's already included in
 |   SUB_LIST)
 | - Use %%DATADIR%% in pkg-plist
 | - Use %%JAVA_VERSION%% in the launcher shell script (in case the user
 |   wants to override JAVA_VERSION whe building the port)
 | - Comment the patch
 | - Add a $FreeBSD$ tag in pkg-plist and the patch file
 | - Makefile should not contain editor hints (ex:ts=8)
 | - Use INSTALL_DATA rather than CP when installing JAR files
 
 Again, thanks for the reviewed port and for the detailed
 description. It's a pleasure to work with committers like you,
 really!
 
 | There is one more issue I could not handle: portlint reports that the
 | pkg-descr in too long (30 lines when the maximum length is 24 lines).
 
 portlint says "make it shorter, if possible". It's not that
 long, just a few lines over the suggested maximum :)
 
 I edited the pkg-descr and now it's 27 lines ... would you
 accept it now?
 
 | Could you please review the new version and fix pkg-descr?
 | 
 | Herve
 |
 +----]
 
 [ shar archive snipped ]
 
 Attached is the shar archive containing the minimally
 modified pkg-descr :)
 
 Fernan
 
 PS: I'm just getting over a plane in a few hours, and will
 not be available for a couple of weeks. If you need my
 approval for anything, let things stand for a while if
 they're important. If they're trivial fixes, you have my
 authorization to commit using your criteria. Thanks again!
 
 --yrj/dFKFPuw6o+aM
 Content-Type: application/x-shar
 Content-Disposition: attachment; filename="jalview.shar"
 Content-Transfer-Encoding: quoted-printable
 
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 fo=0Ased 's/^X//' >jalview/distinfo << 'END-of-jalview/distinfo'=0AXMD5 (ja=
 lview_2_07.tar.gz) =3D 48261fc1c2dc011fe8788368c8bf8223=0AXSHA256 (jalview_=
 2_07.tar.gz) =3D 2cc6b5ec40cf45b0e8e8048b98eacb14af230db6ed6929b95bec4ce079=
 2a51f7=0AXSIZE (jalview_2_07.tar.gz) =3D 8439780=0AEND-of-jalview/distinfo=
 =0Aecho x - jalview/pkg-descr=0Ased 's/^X//' >jalview/pkg-descr << 'END-of-=
 jalview/pkg-descr'=0AXJalview is a multiple alignment editor written in Jav=
 a. It is used=0AXwidely in a variety of web pages (e.g. the EBI Clustalw se=
 rver and the=0AXPfam protein domain database) and is also available as a ge=
 neral purpose=0AXalignment editor. =0AX=0AXo Reads and writes alignments in=
  a variety of formats =0AXo Gaps can be inserted/deleted using the mouse.=
 =0AXo Group editing (insertion deletion of gaps in groups of sequences).=0A=
 Xo Removal of gapped columns.=0AXo Align sequences using Web Services (Clus=
 tal, Muscle...)=0AXo Amino acid conservation analysis similar to that of AM=
 AS.=0AXo Alignment sorting options (by name, tree order, percent identity, =
 group).=0AXo UPGMA and NJ trees calculated and drawn based on percent ident=
 ity distances.=0AXo Sequence clustering using principal component analysis.=
 =0AXo Removal of redundant sequences.=0AXo Smith Waterman pairwise alignmen=
 t of selected sequences.=0AXo Web based secondary structure prediction prog=
 rams (JNet).=0AXo User predefined or custom colour schemes to colour alignm=
 ents or groups.=0AXo Sequence feature retrieval and display on the alignmen=
 t.=0AXo Print your alignment with colours and annotations.=0AXo Output alig=
 nments as HTML pages, images (PNG) or postscript (EPS).=0AX=0AXIf you use J=
 alview in your work, please quote this publication.=0AXClamp, M., et al. (2=
 004), The Jalview Java Alignment Editor.=0AXBioinformatics, 12, 426-7 =0AX=
 =0AXWWW: http://www.jalview.org=0AEND-of-jalview/pkg-descr=0Aecho x - jalvi=
 ew/pkg-plist=0Ased 's/^X//' >jalview/pkg-plist << 'END-of-jalview/pkg-plist=
 '=0AX@comment $FreeBSD$=0AXbin/jalview=0AX%%DATADIR%%/activation.jar=0AX%%D=
 ATADIR%%/xercesImpl.jar=0AX%%DATADIR%%/wsdl4j.jar=0AX%%DATADIR%%/saaj.jar=
 =0AX%%DATADIR%%/regex.jar=0AX%%DATADIR%%/mail.jar=0AX%%DATADIR%%/log4j-1.2.=
 8.jar=0AX%%DATADIR%%/jhall.jar=0AX%%DATADIR%%/jaxrpc.jar=0AX%%DATADIR%%/jal=
 view.jar=0AX%%DATADIR%%/commons-logging.jar=0AX%%DATADIR%%/commons-discover=
 y.jar=0AX%%DATADIR%%/castor-0.9.6-xml.jar=0AX%%DATADIR%%/axis.jar=0AX%%DATA=
 DIR%%/xml-apis.jar=0AX@dirrm %%DATADIR%%=0AEND-of-jalview/pkg-plist=0Aecho =
 c - jalview/files=0Amkdir -p jalview/files > /dev/null 2>&1=0Aecho x - jalv=
 iew/files/patch-build.xml=0Ased 's/^X//' >jalview/files/patch-build.xml << =
 'END-of-jalview/files/patch-build.xml'=0AX$FreeBSD$=0AX=0AXThis patch remov=
 es the webstart support.=0AX=0AX--- build.xml.orig	Mon Dec 12 14:57:02 2005=
 =0AX+++ build.xml	Fri Jan 27 12:20:52 2006=0AX@@ -180,6 +180,10 @@=0AX     =
     </fileset>=0AX       </copy>=0AX <!-- the default keystore details migh=
 t need to be edited here -->=0AX+<!-- Remove all the remaining stuff for th=
 is target =0AX+     which is only necessary if we want to start jalview=0AX=
 +     using java web start. It requires us to generate a key =0AX+     befo=
 re building the port - Fernan - 27.Jan.2006 =0AX       <signjar=0AX       s=
 torepass=3D"alignmentisfun"=0AX       keypass=3D"alignmentisfun"=0AX@@ -194=
 ,8 +198,9 @@=0AX       </fileset>=0AX       </signjar>=0AX       <taskdef c=
 lasspathref=3D"build.classpath" resource=3D"com/roxes/tools/ant/taskdefs.pr=
 operties"/>=0AX-=0AX+-->=0AX       <!--    codebase=3D"http://www.jalview.o=
 rg/jalview/webstart" -->=0AX+<!--=0AX       <jnlp toFile=3D"${packageDir}/j=
 alview.jnlp" href=3D"jalview.jnlp"=0AX       codebase=3D"${WebStartLocation=
 }">=0AX       <information>=0AX@@ -206,6 +211,7 @@=0AX         <description=
  kind=3D"short">Jalview</description>=0AX         <icon href=3D"logo_big.gi=
 f"/>=0AX         <offline_allowed/>=0AX+-->=0AX 	<!--=0AX 	<association mim=
 e-type=3D"application-x/ext-file" extensions=3D"fa"/>=0AX         <associat=
 ion mime-type=3D"application-x/ext-file" extensions=3D"fasta"/>=0AX@@ -216,=
 6 +222,7 @@=0AX         <association mime-type=3D"application-x/ext-file" e=
 xtensions=3D"aln"/>=0AX         <association mime-type=3D"application-x/ext=
 -file" extensions=3D"pir"/>=0AX 	-->=0AX+<!--=0AX        </information>=0AX=
          <resources>=0AX           <j2se version=3D"1.4+"/>=0AX@@ -234,6 +2=
 41,7 @@=0AX           <all_permissions/>=0AX         </security>=0AX       =
 </jnlp>=0AX+-->=0AX     </target>=0AX     <target name=3D"runenv" depends=
 =3D"init">=0AX       <path id=3D"run.classpath">=0AEND-of-jalview/files/pat=
 ch-build.xml=0Aecho x - jalview/files/jalview.sh.in=0Ased 's/^X//' >jalview=
 /files/jalview.sh.in << 'END-of-jalview/files/jalview.sh.in'=0AX#!/bin/sh=
 =0AX#=0AX# $FreeBSD$=0AX=0AX# Shell script to launch jalview using our java=
 vm wrapper=0AX=0AXJAVA_VERSION=3D"%%JAVA_VERSION%%" "%%LOCALBASE%%/bin/java=
 " -Djava.ext.dirs=3D"%%DATADIR%%" -cp "%%DATADIR%%/jalview.jar" jalview.bin=
 =2EJalview=0AEND-of-jalview/files/jalview.sh.in=0Aexit=0A=0A
 --yrj/dFKFPuw6o+aM--
State-Changed-From-To: feedback->closed 
State-Changed-By: hq 
State-Changed-When: Mon Feb 13 09:42:45 UTC 2006 
State-Changed-Why:  
New port added. 

I reduced pkg-descr to 25 lines by justifying the text a bit more (line length 
can be up to 80 characters). 

Thanks for your contribution! 

http://www.freebsd.org/cgi/query-pr.cgi?pr=93054 
>Unformatted:
