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