63 lines
2.6 KiB
Makefile
63 lines
2.6 KiB
Makefile
# $FreeBSD$
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PORTNAME= cytoscape
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DISTVERSION= 3.6.1
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CATEGORIES= biology java
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MASTER_SITES= LOCAL/yuri/:maven \
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http://people.freebsd.org/~yuri/:maven
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DISTFILES= FreeBSD-${PORTNAME}-${PORTVERSION}-maven-repository.tar.gz:maven
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MAINTAINER= yuri@FreeBSD.org
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COMMENT= Software to visualize molecular interaction networks, gene expression
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LICENSE= LGPL21
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LICENSE_FILE= ${WRKSRC}/api/LICENSE
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BROKEN_aarch64= fails to build: Cytoscape Third-Party Dependencies (third-party): FAILURE
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BROKEN_armv6= fails to build: Cytoscape Third-Party Dependencies (third-party): FAILURE
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BROKEN_armv7= fails to build: Cytoscape Third-Party Dependencies (third-party): FAILURE
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BUILD_DEPENDS= mvn:devel/maven \
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bash:shells/bash
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RUN_DEPENDS= bash:shells/bash
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USES= shebangfix
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SHEBANG_FILES= gui-distribution/assembly/src/main/bin/cytoscape.sh
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USE_JAVA= yes
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JAVA_VERSION= 1.7+
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USE_GITHUB= yes
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GH_TUPLE= ${PORTNAME}:${PORTNAME}-parent:${DISTVERSION}:p/parent \
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${PORTNAME}:${PORTNAME}-api:${DISTVERSION}:a/api \
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${PORTNAME}:${PORTNAME}-impl:${DISTVERSION}:i/impl \
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${PORTNAME}:${PORTNAME}-support:${DISTVERSION}:s/support \
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${PORTNAME}:${PORTNAME}-gui-distribution:${DISTVERSION}:g/gui-distribution \
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${PORTNAME}:${PORTNAME}-app-template:${DISTVERSION}:d/app-developer
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NO_ARCH= yes
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USER_WRKDIR= ~/.${PORTNAME}
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do-build:
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@cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} \
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${LOCALBASE}/bin/mvn --offline \
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-fae install \
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-Dmaven.test.skip=true \
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-Duser.home=${WRKDIR}
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do-install:
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@cd ${WRKSRC} && ${COPYTREE_SHARE} gui-distribution ${STAGEDIR}${DATADIR}
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# shouldn't be needed, but the executable bit sometimes isn't set
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@${CHMOD} +x ${STAGEDIR}${DATADIR}/gui-distribution/assembly/target/cytoscape/cytoscape.sh
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@${CHMOD} +x ${STAGEDIR}${DATADIR}/gui-distribution/assembly/target/cytoscape/framework/bin/karaf
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# create a shell executable calling the real command
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@(echo "#!/bin/sh"; \
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echo ""; \
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echo "cd ${DATADIR} && JAVA_HOME=${JAVA_HOME} ./gui-distribution/assembly/target/cytoscape/cytoscape.sh \"$@\"" \
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) > ${STAGEDIR}${PREFIX}/bin/${PORTNAME}
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@${CHMOD} +x ${STAGEDIR}${PREFIX}/bin/${PORTNAME}
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# redirect user data to /tmp until they fix the location so that it would write under $HOME
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@${RM} -r ${STAGEDIR}${DATADIR}/gui-distribution/assembly/target/cytoscape/framework/instances
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@cd ${STAGEDIR}${DATADIR}/gui-distribution/assembly/target/cytoscape/framework && ${LN} -s /tmp instances
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# use the automatic plist: a few hundred files are under DATADIR
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@${SETENV} ${CO_ENV} ${SH} ${SCRIPTSDIR}/check-stagedir.sh makeplist | ${GREP} -v ^\/ | ${SED} -e 's|%%DATADIR%%|share/${PORTNAME}|' > ${TMPPLIST}
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.include <bsd.port.mk>
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