biology/ncbi-entrez-direct: Access to the NCBI's interconnected databases
Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window.
This commit is contained in:
Jason W. Bacon
parent
0af455342e
commit
ab50f8435a
11 changed files with 268 additions and 0 deletions
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@ -84,6 +84,7 @@
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SUBDIR += muscle
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SUBDIR += ncbi-blast+
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SUBDIR += ncbi-cxx-toolkit
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SUBDIR += ncbi-entrez-direct
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SUBDIR += ncbi-toolkit
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SUBDIR += ncbi-vdb
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SUBDIR += ngs-sdk
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81
biology/ncbi-entrez-direct/Makefile
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81
biology/ncbi-entrez-direct/Makefile
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@ -0,0 +1,81 @@
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PORTNAME= ncbi-entrez-direct
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DISTVERSION= 14.9.20210423
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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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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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USES= go:modules perl5 shebangfix
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USE_GITHUB= nodefault
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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/go-build
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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/${GLSD}/x/sys
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SHEBANG_FILES= nquire edirect.pl word-at-a-time accn-at-a-time \
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amino-acid-composition between-two-genes exclude-uid-lists \
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filter-stop-words intersect-uid-lists phrase-search \
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skip-if-file-exists theme-aliases
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PSCRIPTS= efetch efilter einfo elink epost esearch esummary nquire
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SCRIPTS= accn-at-a-time amino-acid-composition archive-pubmed \
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between-two-genes download-ncbi-data download-pubmed \
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download-sequence efetch efilter einfo elink epost \
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esample esearch esummary exclude-uid-lists expand-current \
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fetch-pubmed filter-stop-words gbf2xml index-extras \
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index-pubmed intersect-uid-lists join-into-groups-of \
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nquire phrase-search pm-collect pm-index pm-invert pm-merge \
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pm-prepare pm-promote pm-refresh pm-stash rchive \
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reorder-columns run-ncbi-converter skip-if-file-exists \
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ecommon.sh sort-uniq-count sort-uniq-count-rank stream-pubmed \
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theme-aliases transmute word-at-a-time xml2tbl xtract xy-plot \
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hlp-xtract.txt transmute xml2json xtract
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post-extract:
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@${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 && ${FILESDIR}/go-build
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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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${INSTALL_SCRIPT} ${FILESDIR}/edirect-test.sh ${STAGEDIR}${PREFIX}/bin
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.include <bsd.port.mk>
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23
biology/ncbi-entrez-direct/distinfo
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23
biology/ncbi-entrez-direct/distinfo
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@ -0,0 +1,23 @@
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TIMESTAMP = 1619301195
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SHA256 (edirect-14.9.20210423/edirect.tar.gz) = 9d6534226164fc5dfae7abcf25bfdbd08db068b27f1c13b8a3c4681cda5b0cea
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SIZE (edirect-14.9.20210423/edirect.tar.gz) = 829737
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SHA256 (edirect-14.9.20210423/fatih-color-v1.10.0_GH0.tar.gz) = a00342a7ffb8b119346dce56e152a111cbb9eab3970c429cc2ed4272aec2858e
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SIZE (edirect-14.9.20210423/fatih-color-v1.10.0_GH0.tar.gz) = 1267532
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SHA256 (edirect-14.9.20210423/surgebase-porter2-56e4718818e8_GH0.tar.gz) = d06994daa4d561c2ab477a7072bb7e40a8d39904c88ebf649a1b89105aabdf35
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SIZE (edirect-14.9.20210423/surgebase-porter2-56e4718818e8_GH0.tar.gz) = 156593
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SHA256 (edirect-14.9.20210423/gedex-inflector-16278e9db813_GH0.tar.gz) = d872f3fb5fcc8d8ff25e915670f7ce867a035cfd7a38a2e01ef1550f8770331b
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SIZE (edirect-14.9.20210423/gedex-inflector-16278e9db813_GH0.tar.gz) = 6784
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SHA256 (edirect-14.9.20210423/klauspost-cpuid-v1.3.1_GH0.tar.gz) = 3bf2da7358c8ed33c05bac2ca733749ade03eadf184d81cc7b16fcbe2e230f1d
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SIZE (edirect-14.9.20210423/klauspost-cpuid-v1.3.1_GH0.tar.gz) = 367144
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SHA256 (edirect-14.9.20210423/pbnjay-memory-b12e5d931931_GH0.tar.gz) = 8903a451771edca578c2aa09848f23027dc02df2c67f675f4dd1aae257a71ad6
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SIZE (edirect-14.9.20210423/pbnjay-memory-b12e5d931931_GH0.tar.gz) = 3076
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SHA256 (edirect-14.9.20210423/mattn-go-colorable-v0.1.8_GH0.tar.gz) = 1027954f9abbe06b6e117e3047af70204dd0eb4f8c27fcd459fb2574b279755f
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SIZE (edirect-14.9.20210423/mattn-go-colorable-v0.1.8_GH0.tar.gz) = 9571
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SHA256 (edirect-14.9.20210423/mattn-go-isatty-v0.0.12_GH0.tar.gz) = addbdc341d7685ed4cc8d2d8a8fd2bd9b784bde00d0ea99fb251039fc10c611c
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SIZE (edirect-14.9.20210423/mattn-go-isatty-v0.0.12_GH0.tar.gz) = 4548
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SHA256 (edirect-14.9.20210423/fiam-gounidecode-8deddbd03fec_GH0.tar.gz) = b763f4eb0d0f130821b52484565b32bae1585c4cb0edc57adb94f13b67765176
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SIZE (edirect-14.9.20210423/fiam-gounidecode-8deddbd03fec_GH0.tar.gz) = 190666
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SHA256 (edirect-14.9.20210423/golang-text-v0.3.5_GH0.tar.gz) = f85d1185ba116cd40ef8cf702fe1d960ed41d039c08fd314dbeb5866f3166f27
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SIZE (edirect-14.9.20210423/golang-text-v0.3.5_GH0.tar.gz) = 8348127
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SHA256 (edirect-14.9.20210423/golang-sys-d5e6a3e2c0ae_GH0.tar.gz) = 6cd44aa33cb0fc4caedadde44b3a943bece0aa67d803c00bfb09b03222845f19
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SIZE (edirect-14.9.20210423/golang-sys-d5e6a3e2c0ae_GH0.tar.gz) = 1539001
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33
biology/ncbi-entrez-direct/files/edirect-test.sh
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33
biology/ncbi-entrez-direct/files/edirect-test.sh
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#!/bin/sh -ex
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##########################################################################
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# Function description:
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# Pause until user presses return
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##########################################################################
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pause()
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{
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local junk
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printf "Press return to continue..."
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read junk
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}
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esearch -db pubmed -query "opsin gene conversion" | \
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elink -related | \
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elink -target protein
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pause
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esearch -db pubmed -query "lycopene cyclase" | efetch -format abstract
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pause
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esearch -db protein -query "lycopene cyclase" | efetch -format fasta
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pause
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esearch -db pubmed -query "opsin gene conversion" | \
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elink -related | efilter -query "tetrachromacy"
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pause
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efilter -days 60 -datetype PDAT
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efilter -mindate 1990 -maxdate 1999 -datetype PDAT
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7
biology/ncbi-entrez-direct/files/go-build
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7
biology/ncbi-entrez-direct/files/go-build
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#!/bin/sh -ex
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platform=`uname -s`
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export HOME=$(pwd)
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go build -o xtract."$platform" xtract.go
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go build -o transmute."$platform" transmute.go
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go build -o rchive."$platform" rchive.go
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33
biology/ncbi-entrez-direct/files/modules.txt
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33
biology/ncbi-entrez-direct/files/modules.txt
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@ -0,0 +1,33 @@
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# eutils v0.0.0-00010101000000-000000000000 => ../eutils
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## explicit
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eutils
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# github.com/fatih/color v1.10.0
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## explicit
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github.com/fatih/color
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# github.com/fiam/gounidecode v0.0.0-20150629112515-8deddbd03fec
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## explicit
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github.com/fiam/gounidecode/unidecode
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# github.com/gedex/inflector v0.0.0-20170307190818-16278e9db813
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github.com/gedex/inflector
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# github.com/klauspost/cpuid v1.3.1
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github.com/klauspost/cpuid
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# github.com/mattn/go-colorable v0.1.8
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github.com/mattn/go-colorable
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# github.com/mattn/go-isatty v0.0.12
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github.com/mattn/go-isatty
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# github.com/pbnjay/memory v0.0.0-20201129165224-b12e5d931931
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github.com/pbnjay/memory
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# github.com/stretchr/testify v1.7.0
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## explicit
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# github.com/surge/glog v0.0.0-20141108051140-2578deb2b95c
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## explicit
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# github.com/surgebase/porter2 v0.0.0-20150829210152-56e4718818e8
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## explicit
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github.com/surgebase/porter2
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# golang.org/x/sys v0.0.0-20200223170610-d5e6a3e2c0ae
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golang.org/x/sys/unix
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# golang.org/x/text v0.3.5
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golang.org/x/text/runes
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golang.org/x/text/transform
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golang.org/x/text/unicode/norm
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# eutils => ../eutils
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10
biology/ncbi-entrez-direct/files/patch-rchive
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10
biology/ncbi-entrez-direct/files/patch-rchive
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@ -0,0 +1,10 @@
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--- rchive.orig 2021-03-04 06:50:29 UTC
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+++ rchive
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@@ -43,6 +43,7 @@ case "$osname-$cputype" in
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Darwin-*arm* ) platform=Darwin ;;
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CYGWIN_NT-* | MINGW*-* ) platform=CYGWIN_NT ;;
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Linux-*arm* ) platform=ARM ;;
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+ FreeBSD-* ) platform=FreeBSD ;;
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* ) platform=UNSUPPORTED ;;
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esac
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compiled=$0."$platform"
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10
biology/ncbi-entrez-direct/files/patch-transmute
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10
biology/ncbi-entrez-direct/files/patch-transmute
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@ -0,0 +1,10 @@
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--- transmute.orig 2021-03-04 06:50:29 UTC
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+++ transmute
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@@ -329,6 +329,7 @@ case "$osname-$cputype" in
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Darwin-*arm* ) platform=Darwin ;;
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CYGWIN_NT-* | MINGW*-* ) platform=CYGWIN_NT ;;
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Linux-*arm* ) platform=ARM ;;
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+ FreeBSD-* ) platform=FreeBSD ;;
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* ) platform=UNSUPPORTED ;;
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esac
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compiled=$0."$platform"
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10
biology/ncbi-entrez-direct/files/patch-xtract
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10
biology/ncbi-entrez-direct/files/patch-xtract
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@ -0,0 +1,10 @@
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--- xtract.orig 2018-04-02 18:50:22 UTC
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+++ xtract
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@@ -8,6 +8,7 @@ case "$osname-$cputype" in
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Darwin-x86_64 ) platform=Darwin ;;
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CYGWIN_NT-* | MINGW*-* ) platform=CYGWIN_NT ;;
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Linux-*arm* ) platform=ARM ;;
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+ FreeBSD-* ) platform=FreeBSD ;;
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* ) platform=UNSUPPORTED ;;
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esac
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compiled=$0."$platform"
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5
biology/ncbi-entrez-direct/pkg-descr
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5
biology/ncbi-entrez-direct/pkg-descr
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Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected
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databases (publication, sequence, structure, gene, variation, expression, etc.)
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from a UNIX terminal window.
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WWW: https://www.ncbi.nlm.nih.gov/books/NBK179288/
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55
biology/ncbi-entrez-direct/pkg-plist
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55
biology/ncbi-entrez-direct/pkg-plist
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bin/accn-at-a-time
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bin/amino-acid-composition
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bin/archive-pubmed
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bin/between-two-genes
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bin/download-ncbi-data
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bin/download-pubmed
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bin/download-sequence
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bin/ecommon.sh
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bin/edirect-test.sh
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bin/edirect.pl
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bin/efetch
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bin/efilter
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bin/einfo
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bin/elink
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bin/epost
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bin/esample
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bin/esearch
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bin/esummary
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bin/exclude-uid-lists
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bin/expand-current
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bin/fetch-pubmed
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bin/filter-stop-words
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bin/gbf2xml
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bin/hlp-xtract.txt
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bin/index-extras
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bin/index-pubmed
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bin/intersect-uid-lists
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bin/join-into-groups-of
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bin/nquire
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bin/phrase-search
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bin/pm-collect
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bin/pm-index
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bin/pm-invert
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bin/pm-merge
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bin/pm-prepare
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bin/pm-promote
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bin/pm-refresh
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bin/pm-stash
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bin/rchive
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bin/rchive.FreeBSD
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bin/reorder-columns
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bin/run-ncbi-converter
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bin/skip-if-file-exists
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bin/sort-uniq-count
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bin/sort-uniq-count-rank
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bin/stream-pubmed
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bin/theme-aliases
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bin/transmute
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bin/transmute.FreeBSD
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bin/word-at-a-time
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bin/xml2json
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bin/xml2tbl
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bin/xtract
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bin/xtract.FreeBSD
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bin/xy-plot
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