87 lines
3.2 KiB
Makefile
87 lines
3.2 KiB
Makefile
PORTNAME= ncbi-entrez-direct
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DISTVERSION= 14.9.20210423
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PORTREVISION= 9
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CATEGORIES= biology perl5
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MASTER_SITES= ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/${PORTVERSION}/
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DISTFILES= edirect.tar.gz
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DIST_SUBDIR= edirect-${PORTVERSION}
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MAINTAINER= jwb@FreeBSD.org
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COMMENT= Access to the NCBI's suite of interconnected databases
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WWW= https://www.ncbi.nlm.nih.gov/books/NBK179288/
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LICENSE= PD
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BUILD_DEPENDS= bash:shells/bash
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RUN_DEPENDS= p5-libwww>=0:www/p5-libwww \
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p5-LWP-Protocol-https>=0:www/p5-LWP-Protocol-https \
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p5-XML-Simple>=0:textproc/p5-XML-Simple \
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curl:ftp/curl
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USES= go:modules perl5 shebangfix
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USE_GITHUB= nodefault
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CONFLICTS_INSTALL= ebook-tools p5-XML-Compile # bin/einfo bin/xml2json
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# Dependency versions:
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# make clean extract
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# cd ${WRKSRC}/cmd
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# rm -r vendor
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# ../../../files/build-cmd
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# files/modules.txt: cd ${WRKSRC}/cmd && go mod vendor
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GHSD= vendor/github.com
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GLSD= vendor/golang.org
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GH_TUPLE= fatih:color:v1.10.0:a/${GHSD}/fatih/color \
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surgebase:porter2:56e4718818e8:b/${GHSD}/surgebase/porter2 \
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gedex:inflector:16278e9db813:c/${GHSD}/gedex/inflector \
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klauspost:cpuid:v1.3.1:d/${GHSD}/klauspost/cpuid \
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pbnjay:memory:b12e5d931931:e/${GHSD}/pbnjay/memory \
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mattn:go-colorable:v0.1.8:f/${GHSD}/mattn/go-colorable \
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mattn:go-isatty:v0.0.12:g/${GHSD}/mattn/go-isatty \
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fiam:gounidecode:8deddbd03fec:h/${GHSD}/fiam/gounidecode \
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golang:text:v0.3.5:i/${GLSD}/x/text \
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golang:sys:d5e6a3e2c0ae:j/${GLSD}/x/sys
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SHEBANG_FILES= nquire edirect.pl word-at-a-time accn-at-a-time \
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amino-acid-composition between-two-genes exclude-uid-lists \
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filter-stop-words intersect-uid-lists phrase-search \
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skip-if-file-exists theme-aliases test-edirect hgvs2spdi
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PSCRIPTS= efetch efilter einfo elink epost esearch esummary nquire
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SCRIPTS= accn-at-a-time amino-acid-composition archive-pubmed \
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between-two-genes download-ncbi-data download-pubmed \
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download-sequence efetch efilter einfo elink epost \
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esample esearch esummary exclude-uid-lists expand-current \
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fetch-pubmed filter-stop-words gbf2xml index-extras \
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index-pubmed intersect-uid-lists join-into-groups-of \
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nquire phrase-search pm-collect pm-index pm-invert pm-merge \
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pm-prepare pm-promote pm-refresh pm-stash rchive \
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reorder-columns run-ncbi-converter skip-if-file-exists \
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ecommon.sh sort-uniq-count sort-uniq-count-rank stream-pubmed \
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theme-aliases transmute word-at-a-time xml2tbl xtract xy-plot \
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hlp-xtract.txt transmute xml2json xtract test-edirect \
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align-columns hgvs2spdi sort-table print-columns
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post-extract:
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@${MV} ${WRKDIR}/edirect/* ${WRKSRC}
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@${RMDIR} ${WRKDIR}/edirect
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@${MV} ${WRKSRC}/vendor ${WRKSRC}/cmd
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pre-configure:
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@cd ${WRKSRC} && ${REINPLACE_CMD} \
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-e 's|$$PATH:$$pth|$$PATH:${PREFIX}/bin|g' \
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-e 's|"$$pth"|${PREFIX}/bin|g' \
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${PSCRIPTS}
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do-build:
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@${CP} ${FILESDIR}/modules.txt ${WRKSRC}/cmd/vendor
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@${CP} -R ${WRKSRC}/eutils ${WRKSRC}/cmd/vendor
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@cd ${WRKSRC}/cmd && ${SETENV} ${MAKE_ENV} ${FILESDIR}/build-cmd
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do-install:
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cd ${WRKSRC} && ${INSTALL_SCRIPT} ${SCRIPTS} ${STAGEDIR}${PREFIX}/bin
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${INSTALL_SCRIPT} ${WRKSRC}/edirect.pl ${STAGEDIR}${PREFIX}/bin
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${INSTALL_PROGRAM} ${WRKSRC}/cmd/*.FreeBSD ${STAGEDIR}${PREFIX}/bin
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.include <bsd.port.mk>
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