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| author | Jason W. Bacon <jwb@FreeBSD.org> | 2021-04-25 17:18:38 +0000 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2021-04-25 17:18:38 +0000 |
| commit | 6b63ef7436c4e0ec7693779240f1c90fa6e57a57 (patch) | |
| tree | 0125bac2d6bb5d5ef4a2a99c966fc3329942b4aa /biology/ucsc-userapps/Makefile | |
| parent | e8530452e7f432b4b8e1da82e9d139418c293985 (diff) | |
| download | ports-6b63ef7436c4e0ec7693779240f1c90fa6e57a57.tar.gz ports-6b63ef7436c4e0ec7693779240f1c90fa6e57a57.zip | |
biology/ucsc-userapps: Command line tools from the UCSC Genome Browser project
These are the command-line bioinformatics utilities associated with the UCSC
genome browser. Care has been taken to install only the freely available
tools. However, the license information at https://genome.ucsc.edu/license/
is not entirely clear and we may add non-free utilities in the future.
Contact UCSC if you are using this port for commercial purposes.
Diffstat (limited to 'biology/ucsc-userapps/Makefile')
| -rw-r--r-- | biology/ucsc-userapps/Makefile | 76 |
1 files changed, 76 insertions, 0 deletions
diff --git a/biology/ucsc-userapps/Makefile b/biology/ucsc-userapps/Makefile new file mode 100644 index 000000000000..7a3244c70fcb --- /dev/null +++ b/biology/ucsc-userapps/Makefile @@ -0,0 +1,76 @@ +# Created by: J. Bacon <jwb@FreeBSD.org> + +PORTNAME= ucsc-userapps +DISTVERSION= 413 +CATEGORIES= biology perl5 python +MASTER_SITES= http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/ +DISTNAME= userApps.v${PORTVERSION}.src + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Command line tools from the UCSC Genome Browser project + +LICENSE= UCSC-GB +LICENSE_NAME= UCSC Genome Browser License +LICENSE_TEXT= To the best of our knowledge, all of the tools installed by\ + this port are freely available. However, a license is\ + required for commercial download and installation of some\ + binaries and source code in the UCSC Genome Browser\ + distribution.\n\nContact UCSC directly if you are using these\ + tools for commercial purposes.\n\nSee\ + https://genome.ucsc.edu/license/ for full terms. +LICENSE_PERMS= no-dist-mirror no-dist-sell no-pkg-mirror no-pkg-sell + +ONLY_FOR_ARCHS= amd64 +ONLY_FOR_ARCHS_REASON= _mm_popcnt_u64 + +BUILD_DEPENDS= bash:shells/bash +LIB_DEPENDS= libiconv.so:converters/libiconv \ + libmysqlclient.so:databases/mysql57-client \ + libpng.so:graphics/png +RUN_DEPENDS= bash:shells/bash + +USES= gmake localbase:ldflags shebangfix perl5 python:3.6+ ssl tar:tgz + +RESTRICTED= Redistribution is limited, see license + +SHEBANG_FILES= kent/src/checkUmask.sh \ + kent/src/utils/bigHeat \ + kent/src/utils/chromToUcsc/chromToUcsc \ + kent/src/utils/tdbRename \ + kent/src/utils/tdbSort \ + kent/src/utils/trackDbIndexBb/trackDbIndexBb \ + kent/src/utils/ucscApiClient \ + kent/src/utils/webSync + +WRKSRC= ${WRKDIR}/userApps +CFLAGS+= -fcommon +MAKEFILE= [Mm]akefile +MAKE_ENV= BINDIR=${WRKSRC}/bin + +SUB_FILES= ucsc-shell + +# Build only non-commercial tools +do-build: + @${MV} ${WRKSRC}/kent/src/inc/uuid.h ${WRKSRC}/kent/src/inc/my_uuid.h + @${MKDIR} ${WRKSRC}/bin + @(cd ${WRKSRC}/kent/src/lib && ${DO_MAKE_BUILD}) + @(cd ${WRKSRC}/kent/src/htslib && ${DO_MAKE_BUILD}) + @(cd ${WRKSRC}/kent/src/jkOwnLib && ${DO_MAKE_BUILD}) + @(cd ${WRKSRC}/kent/src/hg/lib && ${DO_MAKE_BUILD}) + @(cd ${WRKSRC}/kent/src/utils && ${DO_MAKE_BUILD}) + +do-install: + @${MKDIR} ${WRKSRC}/scripts ${WRKSRC}/binaries + @${CP} $$(file ${WRKSRC}/bin/* | fgrep ELF | cut -d : -f 1) \ + ${WRKSRC}/binaries + @${CP} $$(file ${WRKSRC}/bin/* | fgrep -v ELF | cut -d : -f 1) \ + ${WRKSRC}/scripts + @${MKDIR} ${STAGEDIR}${PREFIX}/userapps/bin + ${INSTALL_PROGRAM} ${WRKSRC}/binaries/* \ + ${STAGEDIR}${PREFIX}/userapps/bin + ${INSTALL_SCRIPT} ${WRKSRC}/scripts/* \ + ${STAGEDIR}${PREFIX}/userapps/bin + ${INSTALL_SCRIPT} ${WRKDIR}/ucsc-shell \ + ${STAGEDIR}${PREFIX}/bin + +.include <bsd.port.mk> |