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PORTNAME= ncbi-entrez-direct
DISTVERSION= 14.9.20210423
PORTREVISION= 5
CATEGORIES= biology perl5
MASTER_SITES= ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/${PORTVERSION}/
DISTFILES= edirect.tar.gz
DIST_SUBDIR= edirect-${PORTVERSION}
MAINTAINER= jwb@FreeBSD.org
COMMENT= Access to the NCBI's suite of interconnected databases
LICENSE= PD
BUILD_DEPENDS= bash:shells/bash
RUN_DEPENDS= p5-libwww>=0:www/p5-libwww \
p5-LWP-Protocol-https>=0:www/p5-LWP-Protocol-https \
p5-XML-Simple>=0:textproc/p5-XML-Simple \
curl:ftp/curl
USES= go:modules perl5 shebangfix
USE_GITHUB= nodefault
CONFLICTS_INSTALL= ebook-tools p5-XML-Compile # bin/einfo bin/xml2json
# Dependency versions:
# make clean extract
# cd ${WRKSRC}/cmd
# rm -r vendor
# ../../../files/build-cmd
# files/modules.txt: cd ${WRKSRC}/cmd && go mod vendor
GHSD= vendor/github.com
GLSD= vendor/golang.org
GH_TUPLE= fatih:color:v1.10.0:a/${GHSD}/fatih/color \
surgebase:porter2:56e4718818e8:b/${GHSD}/surgebase/porter2 \
gedex:inflector:16278e9db813:c/${GHSD}/gedex/inflector \
klauspost:cpuid:v1.3.1:d/${GHSD}/klauspost/cpuid \
pbnjay:memory:b12e5d931931:e/${GHSD}/pbnjay/memory \
mattn:go-colorable:v0.1.8:f/${GHSD}/mattn/go-colorable \
mattn:go-isatty:v0.0.12:g/${GHSD}/mattn/go-isatty \
fiam:gounidecode:8deddbd03fec:h/${GHSD}/fiam/gounidecode \
golang:text:v0.3.5:i/${GLSD}/x/text \
golang:sys:d5e6a3e2c0ae:j/${GLSD}/x/sys
SHEBANG_FILES= nquire edirect.pl word-at-a-time accn-at-a-time \
amino-acid-composition between-two-genes exclude-uid-lists \
filter-stop-words intersect-uid-lists phrase-search \
skip-if-file-exists theme-aliases test-edirect hgvs2spdi
PSCRIPTS= efetch efilter einfo elink epost esearch esummary nquire
SCRIPTS= accn-at-a-time amino-acid-composition archive-pubmed \
between-two-genes download-ncbi-data download-pubmed \
download-sequence efetch efilter einfo elink epost \
esample esearch esummary exclude-uid-lists expand-current \
fetch-pubmed filter-stop-words gbf2xml index-extras \
index-pubmed intersect-uid-lists join-into-groups-of \
nquire phrase-search pm-collect pm-index pm-invert pm-merge \
pm-prepare pm-promote pm-refresh pm-stash rchive \
reorder-columns run-ncbi-converter skip-if-file-exists \
ecommon.sh sort-uniq-count sort-uniq-count-rank stream-pubmed \
theme-aliases transmute word-at-a-time xml2tbl xtract xy-plot \
hlp-xtract.txt transmute xml2json xtract test-edirect \
align-columns hgvs2spdi sort-table print-columns
post-extract:
@${MV} ${WRKDIR}/edirect/* ${WRKSRC}
@${RMDIR} ${WRKDIR}/edirect
@${MV} ${WRKSRC}/vendor ${WRKSRC}/cmd
pre-configure:
@cd ${WRKSRC} && ${REINPLACE_CMD} \
-e 's|$$PATH:$$pth|$$PATH:${PREFIX}/bin|g' \
-e 's|"$$pth"|${PREFIX}/bin|g' \
${PSCRIPTS}
do-build:
@${CP} ${FILESDIR}/modules.txt ${WRKSRC}/cmd/vendor
@${CP} -R ${WRKSRC}/eutils ${WRKSRC}/cmd/vendor
@cd ${WRKSRC}/cmd && ${SETENV} ${MAKE_ENV} ${FILESDIR}/build-cmd
do-install:
cd ${WRKSRC} && ${INSTALL_SCRIPT} ${SCRIPTS} ${STAGEDIR}${PREFIX}/bin
${INSTALL_SCRIPT} ${WRKSRC}/edirect.pl ${STAGEDIR}${PREFIX}/bin
${INSTALL_PROGRAM} ${WRKSRC}/cmd/*.FreeBSD ${STAGEDIR}${PREFIX}/bin
.include <bsd.port.mk>
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