diff --git a/biology/jalview/Makefile b/biology/jalview/Makefile index 33341bd764c1..f99bd8d81676 100644 --- a/biology/jalview/Makefile +++ b/biology/jalview/Makefile @@ -1,27 +1,73 @@ # Created by: Fernan Aguero PORTNAME= jalview -PORTVERSION= 2.07 -PORTREVISION= 3 +DISTVERSION= 2.11.1.4 CATEGORIES= biology java -MASTER_SITES= http://www.jalview.org/source/ -DISTNAME= ${PORTNAME}_${PORTVERSION:S/./_/} +MASTER_SITES= https://www.jalview.org/source/ +DISTNAME= ${PORTNAME}_${DISTVERSION:S/./_/g} +DISTFILES= ${DISTNAME}${EXTRACT_SUFX} +EXTRACT_ONLY= ${PORTNAME}_${DISTVERSION:S/./_/g}${EXTRACT_SUFX} -MAINTAINER= ports@FreeBSD.org +EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} + +MAINTAINER= yuri@FreeBSD.org COMMENT= Viewer and editor for multiple sequence alignments +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE + +BUILD_DEPENDS= gradle:devel/gradle + USE_JAVA= yes -JAVA_VERSION= 8 -USE_ANT= yes -ALL_TARGET= makejars +JAVA_VERSION= 11 + WRKSRC= ${WRKDIR}/${PORTNAME} +USE_LOCALE= en_US.UTF-8 + DATADIR= ${JAVASHAREDIR}/${PORTNAME} SUB_FILES= jalview.sh +SUB_LIST= JAVA=${JAVA} + +NO_ARCH= yes + +# to rebuild the deps archive: +# 1. set DEV_UPDATE_MODE=yes +# 2. make makesum build +# 3. upload the *-deps archive +# 4. set DEV_UPDATE_MODE=no +# 5. make clean makesum + +DEV_UPDATE_MODE= no + +DEPS_CACHE_DIR= ${WRKDIR} + +.if (${DEV_UPDATE_MODE} == "yes") +post-build: + @cd ${DEPS_CACHE_DIR} && ${TAR} czf ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX} gradle-${PORTNAME} + @${ECHO} "(!!!) Please upload the deps archive: ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}" +.else +MASTER_SITES+= LOCAL/yuri/:deps +DISTFILES+= ${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}:deps +GRADLE_ARGS= --offline + +post-extract: # need a separate extract step because the cache is in /tmp, and not under work/ like with maven + @cd ${DEPS_CACHE_DIR} && ${TAR} xzf ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX} +.endif + +BINARY_ALIAS= git=false java=${JAVA} + +PLIST_FILES= bin/jalview \ + ${DATADIR}/jalview.jar + +do-build: + @cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} gradle \ + --gradle-user-home ${DEPS_CACHE_DIR}/gradle-${PORTNAME} --project-cache-dir ${DEPS_CACHE_DIR}/gradle-${PORTNAME} \ + ${GRADLE_ARGS} --build-cache shadowJar do-install: ${INSTALL_SCRIPT} ${WRKDIR}/jalview.sh ${STAGEDIR}${PREFIX}/bin/jalview @${MKDIR} ${STAGEDIR}${DATADIR} - ${INSTALL_DATA} ${WRKSRC}/dist/* ${STAGEDIR}${DATADIR} + ${INSTALL_DATA} ${WRKSRC}/build/libs/jalview-all-${DISTVERSION}-j${JAVA_VERSION}.jar ${STAGEDIR}${DATADIR}/jalview.jar .include diff --git a/biology/jalview/distinfo b/biology/jalview/distinfo index a92579a7f909..1a5fba7ea4d9 100644 --- a/biology/jalview/distinfo +++ b/biology/jalview/distinfo @@ -1,2 +1,5 @@ -SHA256 (jalview_2_07.tar.gz) = 2cc6b5ec40cf45b0e8e8048b98eacb14af230db6ed6929b95bec4ce0792a51f7 -SIZE (jalview_2_07.tar.gz) = 8439780 +TIMESTAMP = 1619390838 +SHA256 (jalview_2_11_1_4.tar.gz) = 30c0a89bbaf58bc5fd15fd7b167768d21cda1431676f28e22669fd5a342396eb +SIZE (jalview_2_11_1_4.tar.gz) = 103154170 +SHA256 (jalview-2.11.1.4-deps.tar.gz) = 93e88557841d295146aa5f9144e22a8774c9699c9a6a43a4a25673148d91c7d9 +SIZE (jalview-2.11.1.4-deps.tar.gz) = 21061379 diff --git a/biology/jalview/files/jalview.sh.in b/biology/jalview/files/jalview.sh.in index 33b1a7e75195..eb25b886f2de 100644 --- a/biology/jalview/files/jalview.sh.in +++ b/biology/jalview/files/jalview.sh.in @@ -1,4 +1,3 @@ #!/bin/sh -# Shell script to launch jalview using our javavm wrapper -"%%LOCALBASE%%/bin/java" -Djava.ext.dirs="%%DATADIR%%" -cp "%%DATADIR%%/jalview.jar" jalview.bin.Jalview +%%JAVA%% -classpath %%DATADIR%% -jar %%DATADIR%%/jalview.jar jalview.bin.Jalview diff --git a/biology/jalview/files/patch-build.xml b/biology/jalview/files/patch-build.xml deleted file mode 100644 index 7d6449347ba4..000000000000 --- a/biology/jalview/files/patch-build.xml +++ /dev/null @@ -1,50 +0,0 @@ -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 @@ - - - -+ - -+ - -+ - - - diff --git a/biology/jalview/pkg-descr b/biology/jalview/pkg-descr index dd89d5cac1a6..4fae9fde95ba 100644 --- a/biology/jalview/pkg-descr +++ b/biology/jalview/pkg-descr @@ -1,25 +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 +WWW: https://www.jalview.org diff --git a/biology/jalview/pkg-plist b/biology/jalview/pkg-plist deleted file mode 100644 index 763d29468ed4..000000000000 --- a/biology/jalview/pkg-plist +++ /dev/null @@ -1,16 +0,0 @@ -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