diff options
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/jalview/Makefile | 31 | ||||
| -rw-r--r-- | biology/jalview/distinfo | 3 | ||||
| -rw-r--r-- | biology/jalview/files/jalview.sh.in | 7 | ||||
| -rw-r--r-- | biology/jalview/files/patch-build.xml | 52 | ||||
| -rw-r--r-- | biology/jalview/pkg-descr | 25 | ||||
| -rw-r--r-- | biology/jalview/pkg-plist | 18 |
7 files changed, 137 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index 453364cbe0fc..fd9dcda8d631 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -29,6 +29,7 @@ SUBDIR += gperiodic SUBDIR += grappa SUBDIR += hmmer + SUBDIR += jalview SUBDIR += kinemage SUBDIR += lamarc SUBDIR += libgenome diff --git a/biology/jalview/Makefile b/biology/jalview/Makefile new file mode 100644 index 000000000000..9596bb7d00e5 --- /dev/null +++ b/biology/jalview/Makefile @@ -0,0 +1,31 @@ +# New ports collection makefile for: jalview +# Date created: 11 Jan 2006 +# Whom: Fernan Aguero <fernan@iib.unsam.edu.ar> +# +# $FreeBSD$ +# + +PORTNAME= jalview +PORTVERSION= 2.07 +CATEGORIES= biology java +MASTER_SITES= http://www.jalview.org/source/ +DISTNAME= ${PORTNAME}_${PORTVERSION:S/./_/} + +MAINTAINER= fernan@iib.unsam.edu.ar +COMMENT= A viewer and editor for multiple sequence alignments + +USE_JAVA= yes +JAVA_VERSION= 1.4+ +USE_ANT= yes +ALL_TARGET= makejars +WRKSRC= ${WRKDIR}/${PORTNAME} + +DATADIR= ${JAVASHAREDIR}/${PORTNAME} +SUB_FILES= jalview.sh + +do-install: + ${INSTALL_SCRIPT} ${WRKDIR}/jalview.sh ${PREFIX}/bin/jalview + @${MKDIR} ${DATADIR} + ${INSTALL_DATA} ${WRKSRC}/dist/* ${DATADIR} + +.include <bsd.port.mk> diff --git a/biology/jalview/distinfo b/biology/jalview/distinfo new file mode 100644 index 000000000000..171be1e810a8 --- /dev/null +++ b/biology/jalview/distinfo @@ -0,0 +1,3 @@ +MD5 (jalview_2_07.tar.gz) = 48261fc1c2dc011fe8788368c8bf8223 +SHA256 (jalview_2_07.tar.gz) = 2cc6b5ec40cf45b0e8e8048b98eacb14af230db6ed6929b95bec4ce0792a51f7 +SIZE (jalview_2_07.tar.gz) = 8439780 diff --git a/biology/jalview/files/jalview.sh.in b/biology/jalview/files/jalview.sh.in new file mode 100644 index 000000000000..0444e47656ea --- /dev/null +++ b/biology/jalview/files/jalview.sh.in @@ -0,0 +1,7 @@ +#!/bin/sh +# +# $FreeBSD$ + +# Shell script to launch jalview using our javavm wrapper + +JAVA_VERSION="%%JAVA_VERSION%%" "%%LOCALBASE%%/bin/java" -Djava.ext.dirs="%%DATADIR%%" -cp "%%DATADIR%%/jalview.jar" jalview.bin.Jalview diff --git a/biology/jalview/files/patch-build.xml b/biology/jalview/files/patch-build.xml new file mode 100644 index 000000000000..d7cd9ab4a814 --- /dev/null +++ b/biology/jalview/files/patch-build.xml @@ -0,0 +1,52 @@ +$FreeBSD$ + +This patch removes the webstart support. + +--- build.xml.orig Mon Dec 12 14:57:02 2005 ++++ build.xml Fri Jan 27 12:20:52 2006 +@@ -180,6 +180,10 @@ + </fileset> + </copy> + <!-- the default keystore details might need to be edited here --> ++<!-- Remove all the remaining stuff for this target ++ which is only necessary if we want to start jalview ++ using java web start. It requires us to generate a key ++ before building the port - Fernan - 27.Jan.2006 + <signjar + storepass="alignmentisfun" + keypass="alignmentisfun" +@@ -194,8 +198,9 @@ + </fileset> + </signjar> + <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties"/> +- ++--> + <!-- codebase="http://www.jalview.org/jalview/webstart" --> ++<!-- + <jnlp toFile="${packageDir}/jalview.jnlp" href="jalview.jnlp" + codebase="${WebStartLocation}"> + <information> +@@ -206,6 +211,7 @@ + <description kind="short">Jalview</description> + <icon href="logo_big.gif"/> + <offline_allowed/> ++--> + <!-- + <association mime-type="application-x/ext-file" extensions="fa"/> + <association mime-type="application-x/ext-file" extensions="fasta"/> +@@ -216,6 +222,7 @@ + <association mime-type="application-x/ext-file" extensions="aln"/> + <association mime-type="application-x/ext-file" extensions="pir"/> + --> ++<!-- + </information> + <resources> + <j2se version="1.4+"/> +@@ -234,6 +241,7 @@ + <all_permissions/> + </security> + </jnlp> ++--> + </target> + <target name="runenv" depends="init"> + <path id="run.classpath"> diff --git a/biology/jalview/pkg-descr b/biology/jalview/pkg-descr new file mode 100644 index 000000000000..74d38570a4e6 --- /dev/null +++ b/biology/jalview/pkg-descr @@ -0,0 +1,25 @@ +Jalview is a multiple alignment editor written in Java. It is used widely in a +variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain +database) and is also available as a general purpose alignment editor. + +o Reads and writes alignments in a variety of formats +o Gaps can be inserted/deleted using the mouse. +o Group editing (insertion deletion of gaps in groups of sequences). +o Removal of gapped columns. +o Align sequences using Web Services (Clustal, Muscle...) +o Amino acid conservation analysis similar to that of AMAS. +o Alignment sorting options (by name, tree order, percent identity, group). +o UPGMA and NJ trees calculated and drawn based on percent identity distances. +o Sequence clustering using principal component analysis. +o Removal of redundant sequences. +o Smith Waterman pairwise alignment of selected sequences. +o Web based secondary structure prediction programs (JNet). +o User predefined or custom colour schemes to colour alignments or groups. +o Sequence feature retrieval and display on the alignment. +o Print your alignment with colours and annotations. +o Output alignments as HTML pages, images (PNG) or postscript (EPS). + +If you use Jalview in your work, please quote this publication. Clamp, M., et +al. (2004), The Jalview Java Alignment Editor. Bioinformatics, 12, 426-7 + +WWW: http://www.jalview.org diff --git a/biology/jalview/pkg-plist b/biology/jalview/pkg-plist new file mode 100644 index 000000000000..203369118cda --- /dev/null +++ b/biology/jalview/pkg-plist @@ -0,0 +1,18 @@ +@comment $FreeBSD$ +bin/jalview +%%DATADIR%%/activation.jar +%%DATADIR%%/xercesImpl.jar +%%DATADIR%%/wsdl4j.jar +%%DATADIR%%/saaj.jar +%%DATADIR%%/regex.jar +%%DATADIR%%/mail.jar +%%DATADIR%%/log4j-1.2.8.jar +%%DATADIR%%/jhall.jar +%%DATADIR%%/jaxrpc.jar +%%DATADIR%%/jalview.jar +%%DATADIR%%/commons-logging.jar +%%DATADIR%%/commons-discovery.jar +%%DATADIR%%/castor-0.9.6-xml.jar +%%DATADIR%%/axis.jar +%%DATADIR%%/xml-apis.jar +@dirrm %%DATADIR%% |