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# Created by: J. Bacon <jwb@FreeBSD.org>
PORTNAME= ucsc-userapps
DISTVERSION= 414
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= Some tools installed by this port require a license for\
commercial use.\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 mostly non-commercial tools. There is some leakage of proprietary
# code from the libraries per conversation with UCSC. Work to resolve this
# is ongoing.
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>
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