Date: Sat, 24 Apr 2021 23:41:10 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: ab50f8435a78 - main - biology/ncbi-entrez-direct: Access to the NCBI's interconnected databases Message-ID: <202104242341.13ONfAJV015117@gitrepo.freebsd.org>
next in thread | raw e-mail | index | archive | help
The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=ab50f8435a78a574ac5ce683004b078c5baf209d commit ab50f8435a78a574ac5ce683004b078c5baf209d Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2021-04-24 23:40:16 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2021-04-24 23:40:16 +0000 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. --- biology/Makefile | 1 + biology/ncbi-entrez-direct/Makefile | 81 ++++++++++++++++++++++++ biology/ncbi-entrez-direct/distinfo | 23 +++++++ biology/ncbi-entrez-direct/files/edirect-test.sh | 33 ++++++++++ biology/ncbi-entrez-direct/files/go-build | 7 ++ biology/ncbi-entrez-direct/files/modules.txt | 33 ++++++++++ biology/ncbi-entrez-direct/files/patch-rchive | 10 +++ biology/ncbi-entrez-direct/files/patch-transmute | 10 +++ biology/ncbi-entrez-direct/files/patch-xtract | 10 +++ biology/ncbi-entrez-direct/pkg-descr | 5 ++ biology/ncbi-entrez-direct/pkg-plist | 55 ++++++++++++++++ 11 files changed, 268 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index 53c31ac00b77..e04fd0d1775a 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -84,6 +84,7 @@ SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-cxx-toolkit + SUBDIR += ncbi-entrez-direct SUBDIR += ncbi-toolkit SUBDIR += ncbi-vdb SUBDIR += ngs-sdk diff --git a/biology/ncbi-entrez-direct/Makefile b/biology/ncbi-entrez-direct/Makefile new file mode 100644 index 000000000000..858e4734786c --- /dev/null +++ b/biology/ncbi-entrez-direct/Makefile @@ -0,0 +1,81 @@ +PORTNAME= ncbi-entrez-direct +DISTVERSION= 14.9.20210423 +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 + +USES= go:modules perl5 shebangfix +USE_GITHUB= nodefault + +# Dependency versions: +# make clean extract +# cd ${WRKSRC}/cmd +# rm -r vendor +# ../../../files/go-build +# 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/${GLSD}/x/sys + +SHEBANG_FILES= nquire edirect.pl word-at-a-time accn-at-a-time \ + amino-acid-composition between-two-genes exclude-uid-lists \ + filter-stop-words intersect-uid-lists phrase-search \ + skip-if-file-exists theme-aliases + +PSCRIPTS= efetch efilter einfo elink epost esearch esummary nquire +SCRIPTS= accn-at-a-time amino-acid-composition archive-pubmed \ + between-two-genes download-ncbi-data download-pubmed \ + download-sequence efetch efilter einfo elink epost \ + esample esearch esummary exclude-uid-lists expand-current \ + fetch-pubmed filter-stop-words gbf2xml index-extras \ + index-pubmed intersect-uid-lists join-into-groups-of \ + nquire phrase-search pm-collect pm-index pm-invert pm-merge \ + pm-prepare pm-promote pm-refresh pm-stash rchive \ + reorder-columns run-ncbi-converter skip-if-file-exists \ + ecommon.sh sort-uniq-count sort-uniq-count-rank stream-pubmed \ + theme-aliases transmute word-at-a-time xml2tbl xtract xy-plot \ + hlp-xtract.txt transmute xml2json xtract + +post-extract: + @${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 && ${FILESDIR}/go-build + +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 new file mode 100644 index 000000000000..be93ed84e5a1 --- /dev/null +++ b/biology/ncbi-entrez-direct/distinfo @@ -0,0 +1,23 @@ +TIMESTAMP = 1619301195 +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 +SIZE (edirect-14.9.20210423/fatih-color-v1.10.0_GH0.tar.gz) = 1267532 +SHA256 (edirect-14.9.20210423/surgebase-porter2-56e4718818e8_GH0.tar.gz) = d06994daa4d561c2ab477a7072bb7e40a8d39904c88ebf649a1b89105aabdf35 +SIZE (edirect-14.9.20210423/surgebase-porter2-56e4718818e8_GH0.tar.gz) = 156593 +SHA256 (edirect-14.9.20210423/gedex-inflector-16278e9db813_GH0.tar.gz) = d872f3fb5fcc8d8ff25e915670f7ce867a035cfd7a38a2e01ef1550f8770331b +SIZE (edirect-14.9.20210423/gedex-inflector-16278e9db813_GH0.tar.gz) = 6784 +SHA256 (edirect-14.9.20210423/klauspost-cpuid-v1.3.1_GH0.tar.gz) = 3bf2da7358c8ed33c05bac2ca733749ade03eadf184d81cc7b16fcbe2e230f1d +SIZE (edirect-14.9.20210423/klauspost-cpuid-v1.3.1_GH0.tar.gz) = 367144 +SHA256 (edirect-14.9.20210423/pbnjay-memory-b12e5d931931_GH0.tar.gz) = 8903a451771edca578c2aa09848f23027dc02df2c67f675f4dd1aae257a71ad6 +SIZE (edirect-14.9.20210423/pbnjay-memory-b12e5d931931_GH0.tar.gz) = 3076 +SHA256 (edirect-14.9.20210423/mattn-go-colorable-v0.1.8_GH0.tar.gz) = 1027954f9abbe06b6e117e3047af70204dd0eb4f8c27fcd459fb2574b279755f +SIZE (edirect-14.9.20210423/mattn-go-colorable-v0.1.8_GH0.tar.gz) = 9571 +SHA256 (edirect-14.9.20210423/mattn-go-isatty-v0.0.12_GH0.tar.gz) = addbdc341d7685ed4cc8d2d8a8fd2bd9b784bde00d0ea99fb251039fc10c611c +SIZE (edirect-14.9.20210423/mattn-go-isatty-v0.0.12_GH0.tar.gz) = 4548 +SHA256 (edirect-14.9.20210423/fiam-gounidecode-8deddbd03fec_GH0.tar.gz) = b763f4eb0d0f130821b52484565b32bae1585c4cb0edc57adb94f13b67765176 +SIZE (edirect-14.9.20210423/fiam-gounidecode-8deddbd03fec_GH0.tar.gz) = 190666 +SHA256 (edirect-14.9.20210423/golang-text-v0.3.5_GH0.tar.gz) = f85d1185ba116cd40ef8cf702fe1d960ed41d039c08fd314dbeb5866f3166f27 +SIZE (edirect-14.9.20210423/golang-text-v0.3.5_GH0.tar.gz) = 8348127 +SHA256 (edirect-14.9.20210423/golang-sys-d5e6a3e2c0ae_GH0.tar.gz) = 6cd44aa33cb0fc4caedadde44b3a943bece0aa67d803c00bfb09b03222845f19 +SIZE (edirect-14.9.20210423/golang-sys-d5e6a3e2c0ae_GH0.tar.gz) = 1539001 diff --git a/biology/ncbi-entrez-direct/files/edirect-test.sh b/biology/ncbi-entrez-direct/files/edirect-test.sh new file mode 100755 index 000000000000..26da1db4ce88 --- /dev/null +++ b/biology/ncbi-entrez-direct/files/edirect-test.sh @@ -0,0 +1,33 @@ +#!/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/files/go-build b/biology/ncbi-entrez-direct/files/go-build new file mode 100755 index 000000000000..d108b7da6209 --- /dev/null +++ b/biology/ncbi-entrez-direct/files/go-build @@ -0,0 +1,7 @@ +#!/bin/sh -ex + +platform=`uname -s` +export HOME=$(pwd) +go build -o xtract."$platform" xtract.go +go build -o transmute."$platform" transmute.go +go build -o rchive."$platform" rchive.go diff --git a/biology/ncbi-entrez-direct/files/modules.txt b/biology/ncbi-entrez-direct/files/modules.txt new file mode 100644 index 000000000000..bf713fd9c42b --- /dev/null +++ b/biology/ncbi-entrez-direct/files/modules.txt @@ -0,0 +1,33 @@ +# eutils v0.0.0-00010101000000-000000000000 => ../eutils +## explicit +eutils +# github.com/fatih/color v1.10.0 +## explicit +github.com/fatih/color +# github.com/fiam/gounidecode v0.0.0-20150629112515-8deddbd03fec +## explicit +github.com/fiam/gounidecode/unidecode +# github.com/gedex/inflector v0.0.0-20170307190818-16278e9db813 +github.com/gedex/inflector +# github.com/klauspost/cpuid v1.3.1 +github.com/klauspost/cpuid +# github.com/mattn/go-colorable v0.1.8 +github.com/mattn/go-colorable +# github.com/mattn/go-isatty v0.0.12 +github.com/mattn/go-isatty +# github.com/pbnjay/memory v0.0.0-20201129165224-b12e5d931931 +github.com/pbnjay/memory +# github.com/stretchr/testify v1.7.0 +## explicit +# github.com/surge/glog v0.0.0-20141108051140-2578deb2b95c +## explicit +# github.com/surgebase/porter2 v0.0.0-20150829210152-56e4718818e8 +## explicit +github.com/surgebase/porter2 +# golang.org/x/sys v0.0.0-20200223170610-d5e6a3e2c0ae +golang.org/x/sys/unix +# golang.org/x/text v0.3.5 +golang.org/x/text/runes +golang.org/x/text/transform +golang.org/x/text/unicode/norm +# eutils => ../eutils diff --git a/biology/ncbi-entrez-direct/files/patch-rchive b/biology/ncbi-entrez-direct/files/patch-rchive new file mode 100644 index 000000000000..1d3657707136 --- /dev/null +++ b/biology/ncbi-entrez-direct/files/patch-rchive @@ -0,0 +1,10 @@ +--- rchive.orig 2021-03-04 06:50:29 UTC ++++ rchive +@@ -43,6 +43,7 @@ case "$osname-$cputype" in + Darwin-*arm* ) platform=Darwin ;; + CYGWIN_NT-* | MINGW*-* ) platform=CYGWIN_NT ;; + Linux-*arm* ) platform=ARM ;; ++ FreeBSD-* ) platform=FreeBSD ;; + * ) platform=UNSUPPORTED ;; + esac + compiled=$0."$platform" diff --git a/biology/ncbi-entrez-direct/files/patch-transmute b/biology/ncbi-entrez-direct/files/patch-transmute new file mode 100644 index 000000000000..198e79551270 --- /dev/null +++ b/biology/ncbi-entrez-direct/files/patch-transmute @@ -0,0 +1,10 @@ +--- transmute.orig 2021-03-04 06:50:29 UTC ++++ transmute +@@ -329,6 +329,7 @@ case "$osname-$cputype" in + Darwin-*arm* ) platform=Darwin ;; + CYGWIN_NT-* | MINGW*-* ) platform=CYGWIN_NT ;; + Linux-*arm* ) platform=ARM ;; ++ FreeBSD-* ) platform=FreeBSD ;; + * ) platform=UNSUPPORTED ;; + esac + compiled=$0."$platform" diff --git a/biology/ncbi-entrez-direct/files/patch-xtract b/biology/ncbi-entrez-direct/files/patch-xtract new file mode 100644 index 000000000000..45e2837e7277 --- /dev/null +++ b/biology/ncbi-entrez-direct/files/patch-xtract @@ -0,0 +1,10 @@ +--- xtract.orig 2018-04-02 18:50:22 UTC ++++ xtract +@@ -8,6 +8,7 @@ case "$osname-$cputype" in + Darwin-x86_64 ) platform=Darwin ;; + CYGWIN_NT-* | MINGW*-* ) platform=CYGWIN_NT ;; + Linux-*arm* ) platform=ARM ;; ++ FreeBSD-* ) platform=FreeBSD ;; + * ) platform=UNSUPPORTED ;; + esac + compiled=$0."$platform" diff --git a/biology/ncbi-entrez-direct/pkg-descr b/biology/ncbi-entrez-direct/pkg-descr new file mode 100644 index 000000000000..b8215012904c --- /dev/null +++ b/biology/ncbi-entrez-direct/pkg-descr @@ -0,0 +1,5 @@ +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. + +WWW: https://www.ncbi.nlm.nih.gov/books/NBK179288/ diff --git a/biology/ncbi-entrez-direct/pkg-plist b/biology/ncbi-entrez-direct/pkg-plist new file mode 100644 index 000000000000..536ba728e03f --- /dev/null +++ b/biology/ncbi-entrez-direct/pkg-plist @@ -0,0 +1,55 @@ +bin/accn-at-a-time +bin/amino-acid-composition +bin/archive-pubmed +bin/between-two-genes +bin/download-ncbi-data +bin/download-pubmed +bin/download-sequence +bin/ecommon.sh +bin/edirect-test.sh +bin/edirect.pl +bin/efetch +bin/efilter +bin/einfo +bin/elink +bin/epost +bin/esample +bin/esearch +bin/esummary +bin/exclude-uid-lists +bin/expand-current +bin/fetch-pubmed +bin/filter-stop-words +bin/gbf2xml +bin/hlp-xtract.txt +bin/index-extras +bin/index-pubmed +bin/intersect-uid-lists +bin/join-into-groups-of +bin/nquire +bin/phrase-search +bin/pm-collect +bin/pm-index +bin/pm-invert +bin/pm-merge +bin/pm-prepare +bin/pm-promote +bin/pm-refresh +bin/pm-stash +bin/rchive +bin/rchive.FreeBSD +bin/reorder-columns +bin/run-ncbi-converter +bin/skip-if-file-exists +bin/sort-uniq-count +bin/sort-uniq-count-rank +bin/stream-pubmed +bin/theme-aliases +bin/transmute +bin/transmute.FreeBSD +bin/word-at-a-time +bin/xml2json +bin/xml2tbl +bin/xtract +bin/xtract.FreeBSD +bin/xy-plot
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?202104242341.13ONfAJV015117>