diff --git a/science/Makefile b/science/Makefile index 2ea460fe7fc48..36ab7506fdc44 100644 --- a/science/Makefile +++ b/science/Makefile @@ -173,6 +173,7 @@ SUBDIR += openmx SUBDIR += opensim-core SUBDIR += openstructure + SUBDIR += opsin SUBDIR += p5-Algorithm-SVMLight SUBDIR += p5-Chemistry-3DBuilder SUBDIR += p5-Chemistry-Bond-Find diff --git a/science/opsin/Makefile b/science/opsin/Makefile new file mode 100644 index 0000000000000..79a4c857bb2ad --- /dev/null +++ b/science/opsin/Makefile @@ -0,0 +1,62 @@ +# $FreeBSD$ + +PORTNAME= opsin +DISTVERSION= 3.0.20190208 +CATEGORIES= science java +MASTER_SITES= https://bitbucket.org/${BB_ACCOUNT}/${PORTNAME}/get/${BB_COMMIT}${EXTRACT_SUFX}?dummy=/:src +DISTFILES= ${PORTNAME}-${DISTVERSION}${EXTRACT_SUFX}:src + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Open Parser for Systematic IUPAC Nomenclature of chemical names + +LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/LICENSE.txt + +BUILD_DEPENDS= mvn:devel/maven + +USE_JAVA= yes + +NO_ARCH= yes + +BB_ACCOUNT= dan2097 +BB_COMMIT= 6688e0cedfcc + +WRKSRC= ${WRKDIR}/${BB_ACCOUNT}-${PORTNAME}-${BB_COMMIT} +SUB_FILES= ${PORTNAME} +SUB_LIST= JAVA=${JAVA} PORTNAME=${PORTNAME} PORTVERSION=${PORTVERSION} + +PLIST_FILES= bin/${PORTNAME} \ + ${JAVAJARDIR}/${PORTNAME}-${PORTVERSION}-jar-with-dependencies.jar + +# to rebuild the deps archive: +# 1. set DEV_UPDATE_MODE=yes +# 2. make makesum build +# 3. upload the *-deps archive +# 4. set DEV_UPDATE_MODE=no +# 5. make clean makesum + +DEV_UPDATE_MODE= no + +.if (${DEV_UPDATE_MODE} == "yes") +post-build: + @cd ${WRKDIR} && ${TAR} czf ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX} .m2 + @${ECHO} "(!!!) Please upload the maven deps archive: ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}" +.else +MASTER_SITES+= LOCAL/yuri/:maven +DISTFILES+= ${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}:maven +MVN_ARGS= --offline +.endif + +do-build: + @cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} \ + ${LOCALBASE}/bin/mvn ${MVN_ARGS} \ + -fae install \ + -Dmaven.test.skip=true \ + -Duser.home=${WRKDIR} \ + package assembly:assembly + +do-install: + ${INSTALL_SCRIPT} ${WRKDIR}/${PORTNAME} ${STAGEDIR}${PREFIX}/bin + ${INSTALL_DATA} ${WRKSRC}/target/${PORTNAME}-*-jar-with-dependencies.jar ${STAGEDIR}${JAVAJARDIR}/${PORTNAME}-${PORTVERSION}-jar-with-dependencies.jar + +.include diff --git a/science/opsin/distinfo b/science/opsin/distinfo new file mode 100644 index 0000000000000..129888a12b23c --- /dev/null +++ b/science/opsin/distinfo @@ -0,0 +1,5 @@ +TIMESTAMP = 1550104217 +SHA256 (opsin-3.0.20190208.tar.gz) = d37222168a0ffb412109095212152f31b0b909abdaa14158561424651426df8f +SIZE (opsin-3.0.20190208.tar.gz) = 1795278 +SHA256 (opsin-3.0.20190208-deps.tar.gz) = b42bfc011571d7e12fbc4e051653d19edaef6b7d04aaa146c817e1309dc4cba2 +SIZE (opsin-3.0.20190208-deps.tar.gz) = 20394666 diff --git a/science/opsin/files/opsin.in b/science/opsin/files/opsin.in new file mode 100644 index 0000000000000..18c1f42382657 --- /dev/null +++ b/science/opsin/files/opsin.in @@ -0,0 +1,5 @@ +#!/bin/sh + +export LC_ALL=en_US.UTF-8 + +%%JAVA%% -jar %%JAVAJARDIR%%/%%PORTNAME%%-%%PORTVERSION%%-jar-with-dependencies.jar "$@" diff --git a/science/opsin/pkg-descr b/science/opsin/pkg-descr new file mode 100644 index 0000000000000..24ddb2751426f --- /dev/null +++ b/science/opsin/pkg-descr @@ -0,0 +1,6 @@ +OPSIN is a Java library for IUPAC name-to-structure conversion offering high +recall and precision on organic chemical nomenclature. +Supported outputs are SMILES, CML (Chemical Markup Language) and InChI (IUPAC +International Chemical Identifier). + +WWW: https://bitbucket.org/dan2097/opsin/src/default/