svn commit: r473806 - in head/biology: . cytoscape

[Yuri Victorovich]

Author: yuri
Date: Tue Jul  3 08:42:54 2018
New Revision: 473806
URL: https://svnweb.freebsd.org/changeset/ports/473806

Log:
  New port: biology/cytoscape: Software to visualize molecular interaction networks, gene expression

Added:
  head/biology/cytoscape/
  head/biology/cytoscape/Makefile   (contents, props changed)
  head/biology/cytoscape/distinfo   (contents, props changed)
  head/biology/cytoscape/pkg-descr   (contents, props changed)
Modified:
  head/biology/Makefile

Modified: head/biology/Makefile
==============================================================================
--- head/biology/Makefile	Tue Jul  3 08:37:35 2018	(r473805)
+++ head/biology/Makefile	Tue Jul  3 08:42:54 2018	(r473806)
@@ -22,6 +22,7 @@
     SUBDIR += clustalw
     SUBDIR += clustalx
     SUBDIR += consed
+    SUBDIR += cytoscape
     SUBDIR += ddocent
     SUBDIR += diamond
     SUBDIR += emboss

Added: head/biology/cytoscape/Makefile
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/cytoscape/Makefile	Tue Jul  3 08:42:54 2018	(r473806)
@@ -0,0 +1,59 @@
+# $FreeBSD$
+
+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 at FreeBSD.org
+COMMENT=	Software to visualize molecular interaction networks, gene expression
+
+LICENSE=	MIT
+xLICENSE_FILE=	${WRKSRC}/license.txt
+
+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
+JAVA_VERSION=	1.7+
+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>

Added: head/biology/cytoscape/distinfo
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/cytoscape/distinfo	Tue Jul  3 08:42:54 2018	(r473806)
@@ -0,0 +1,17 @@
+TIMESTAMP = 1530603760
+SHA256 (FreeBSD-cytoscape-3.6.1-maven-repository.tar.gz) = f3e33e99168b56768d2ee854956e59bcbb888101fd518239887524d692b78f7a
+SIZE (FreeBSD-cytoscape-3.6.1-maven-repository.tar.gz) = 1235655281
+SHA256 (cytoscape-cytoscape-3.6.1_GH0.tar.gz) = f172c9e459293661a83d2618da511901410336b76b0c1716697e60f821c2f150
+SIZE (cytoscape-cytoscape-3.6.1_GH0.tar.gz) = 12785
+SHA256 (cytoscape-cytoscape-parent-3.6.1_GH0.tar.gz) = 0786e8d7877fa54d2a64d65209856a4a946df4facd3cbc947e8c65d14a035084
+SIZE (cytoscape-cytoscape-parent-3.6.1_GH0.tar.gz) = 2863
+SHA256 (cytoscape-cytoscape-api-3.6.1_GH0.tar.gz) = a264a434d5942cad2ef69df7aa29fad74a6d1f11369a964d7c38462608def73b
+SIZE (cytoscape-cytoscape-api-3.6.1_GH0.tar.gz) = 1731631
+SHA256 (cytoscape-cytoscape-impl-3.6.1_GH0.tar.gz) = 0fcea5a4d804972db5b0cf77174a953d22da8fed6740dbaa01754eb7aea50d21
+SIZE (cytoscape-cytoscape-impl-3.6.1_GH0.tar.gz) = 29851040
+SHA256 (cytoscape-cytoscape-support-3.6.1_GH0.tar.gz) = 3f13088c35d41fa616dc7e735469f360ee4d17b1838cde8291f88b01bacfe657
+SIZE (cytoscape-cytoscape-support-3.6.1_GH0.tar.gz) = 52940
+SHA256 (cytoscape-cytoscape-gui-distribution-3.6.1_GH0.tar.gz) = 73fb7efb51a0413252a7e9e28d4fb7e28d16eea9f60be534fd962a5e534ca72e
+SIZE (cytoscape-cytoscape-gui-distribution-3.6.1_GH0.tar.gz) = 14818052
+SHA256 (cytoscape-cytoscape-app-template-3.6.1_GH0.tar.gz) = 9cf7b64a3e6effd22a20d577c7fa41b11f896e2298ef1655f2fe31c21602bce0
+SIZE (cytoscape-cytoscape-app-template-3.6.1_GH0.tar.gz) = 1887

Added: head/biology/cytoscape/pkg-descr
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/cytoscape/pkg-descr	Tue Jul  3 08:42:54 2018	(r473806)
@@ -0,0 +1,6 @@
+Cytoscape is an open source software platform for visualizing complex networks
+and integrating these with any type of attribute data. A lot of Apps are
+available for various kinds of problem domains, including bioinformatics, social
+network analysis, and semantic web.
+
+WWW: http://www.cytoscape.org