Date: Mon, 26 Apr 2021 16:56:39 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: dd7bec771147 - main - biology/ncbi-entrez-direct: Update to 14.9.20210423_1 Message-ID: <202104261656.13QGudSa006529@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=dd7bec77114786adf79d35c325337a59c9684848 commit dd7bec77114786adf79d35c325337a59c9684848 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2021-04-26 16:53:11 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2021-04-26 16:53:11 +0000 biology/ncbi-entrez-direct: Update to 14.9.20210423_1 A few fixes to pass upstream test script --- biology/ncbi-entrez-direct/Makefile | 14 +++++---- biology/ncbi-entrez-direct/distinfo | 2 +- .../files/{go-build => build-cmd} | 3 ++ biology/ncbi-entrez-direct/files/edirect-test.sh | 33 ---------------------- biology/ncbi-entrez-direct/pkg-plist | 6 +++- 5 files changed, 17 insertions(+), 41 deletions(-) diff --git a/biology/ncbi-entrez-direct/Makefile b/biology/ncbi-entrez-direct/Makefile index 858e4734786c..7ece210acd5e 100644 --- a/biology/ncbi-entrez-direct/Makefile +++ b/biology/ncbi-entrez-direct/Makefile @@ -1,5 +1,6 @@ PORTNAME= ncbi-entrez-direct DISTVERSION= 14.9.20210423 +PORTREVISION= 1 CATEGORIES= biology perl5 MASTER_SITES= ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/${PORTVERSION}/ DISTFILES= edirect.tar.gz @@ -13,7 +14,8 @@ 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 + p5-XML-Simple>=0:textproc/p5-XML-Simple \ + curl:ftp/curl USES= go:modules perl5 shebangfix USE_GITHUB= nodefault @@ -22,7 +24,7 @@ USE_GITHUB= nodefault # make clean extract # cd ${WRKSRC}/cmd # rm -r vendor -# ../../../files/go-build +# ../../../files/build-cmd # files/modules.txt: cd ${WRKSRC}/cmd && go mod vendor GHSD= vendor/github.com GLSD= vendor/golang.org @@ -40,7 +42,7 @@ GH_TUPLE= fatih:color:v1.10.0:a/${GHSD}/fatih/color \ 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 + 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 \ @@ -54,7 +56,8 @@ SCRIPTS= accn-at-a-time amino-acid-composition archive-pubmed \ 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 + hlp-xtract.txt transmute xml2json xtract test-edirect \ + align-columns hgvs2spdi sort-table print-columns post-extract: @${MV} ${WRKDIR}/edirect/* ${WRKSRC} @@ -70,12 +73,11 @@ pre-configure: do-build: @${CP} ${FILESDIR}/modules.txt ${WRKSRC}/cmd/vendor @${CP} -R ${WRKSRC}/eutils ${WRKSRC}/cmd/vendor - @cd ${WRKSRC}/cmd && ${FILESDIR}/go-build + @cd ${WRKSRC}/cmd && ${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 - ${INSTALL_SCRIPT} ${FILESDIR}/edirect-test.sh ${STAGEDIR}${PREFIX}/bin .include <bsd.port.mk> diff --git a/biology/ncbi-entrez-direct/distinfo b/biology/ncbi-entrez-direct/distinfo index be93ed84e5a1..e959f316b0e8 100644 --- a/biology/ncbi-entrez-direct/distinfo +++ b/biology/ncbi-entrez-direct/distinfo @@ -1,4 +1,4 @@ -TIMESTAMP = 1619301195 +TIMESTAMP = 1619443745 SHA256 (edirect-14.9.20210423/edirect.tar.gz) = 9d6534226164fc5dfae7abcf25bfdbd08db068b27f1c13b8a3c4681cda5b0cea SIZE (edirect-14.9.20210423/edirect.tar.gz) = 829737 SHA256 (edirect-14.9.20210423/fatih-color-v1.10.0_GH0.tar.gz) = a00342a7ffb8b119346dce56e152a111cbb9eab3970c429cc2ed4272aec2858e diff --git a/biology/ncbi-entrez-direct/files/go-build b/biology/ncbi-entrez-direct/files/build-cmd similarity index 55% rename from biology/ncbi-entrez-direct/files/go-build rename to biology/ncbi-entrez-direct/files/build-cmd index d108b7da6209..1e2ad04bfde9 100755 --- a/biology/ncbi-entrez-direct/files/go-build +++ b/biology/ncbi-entrez-direct/files/build-cmd @@ -1,5 +1,8 @@ #!/bin/sh -ex +# This script replaces setup.sh, which is designed to download GO binaries +# and dependencies and hence does not fit into a package manager build. + platform=`uname -s` export HOME=$(pwd) go build -o xtract."$platform" xtract.go diff --git a/biology/ncbi-entrez-direct/files/edirect-test.sh b/biology/ncbi-entrez-direct/files/edirect-test.sh deleted file mode 100755 index 26da1db4ce88..000000000000 --- a/biology/ncbi-entrez-direct/files/edirect-test.sh +++ /dev/null @@ -1,33 +0,0 @@ -#!/bin/sh -ex - -########################################################################## -# Function description: -# Pause until user presses return -########################################################################## - -pause() -{ - local junk - - printf "Press return to continue..." - read junk -} - -esearch -db pubmed -query "opsin gene conversion" | \ - elink -related | \ - elink -target protein -pause - -esearch -db pubmed -query "lycopene cyclase" | efetch -format abstract -pause - -esearch -db protein -query "lycopene cyclase" | efetch -format fasta -pause - -esearch -db pubmed -query "opsin gene conversion" | \ - elink -related | efilter -query "tetrachromacy" -pause - -efilter -days 60 -datetype PDAT -efilter -mindate 1990 -maxdate 1999 -datetype PDAT - diff --git a/biology/ncbi-entrez-direct/pkg-plist b/biology/ncbi-entrez-direct/pkg-plist index 536ba728e03f..2ef17c29f959 100644 --- a/biology/ncbi-entrez-direct/pkg-plist +++ b/biology/ncbi-entrez-direct/pkg-plist @@ -1,4 +1,5 @@ bin/accn-at-a-time +bin/align-columns bin/amino-acid-composition bin/archive-pubmed bin/between-two-genes @@ -6,7 +7,6 @@ bin/download-ncbi-data bin/download-pubmed bin/download-sequence bin/ecommon.sh -bin/edirect-test.sh bin/edirect.pl bin/efetch bin/efilter @@ -21,6 +21,7 @@ bin/expand-current bin/fetch-pubmed bin/filter-stop-words bin/gbf2xml +bin/hgvs2spdi bin/hlp-xtract.txt bin/index-extras bin/index-pubmed @@ -36,14 +37,17 @@ bin/pm-prepare bin/pm-promote bin/pm-refresh bin/pm-stash +bin/print-columns bin/rchive bin/rchive.FreeBSD bin/reorder-columns bin/run-ncbi-converter bin/skip-if-file-exists +bin/sort-table bin/sort-uniq-count bin/sort-uniq-count-rank bin/stream-pubmed +bin/test-edirect bin/theme-aliases bin/transmute bin/transmute.FreeBSD
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