ncbi-entrez-direct_10.9.20190219+ds-1+b10_amd64.deb


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Description

ncbi-entrez-direct - NCBI Entrez utilities on the command line

Property Value
Distribution Debian 10 (Buster)
Repository Debian Main amd64
Package filename ncbi-entrez-direct_10.9.20190219+ds-1+b10_amd64.deb
Package name ncbi-entrez-direct
Package version 10.9.20190219+ds
Package release 1+b10
Package architecture amd64
Package type deb
Category science
Homepage http://www.ncbi.nlm.nih.gov/books/NBK179288
License -
Maintainer Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Download size 1.55 MB
Installed size 6.49 MB
Entrez Direct (EDirect) is an advanced method for accessing NCBI's set
of interconnected databases (publication, sequence, structure, gene,
variation, expression, etc.) from a terminal window or script.
Functions take search terms from command-line arguments.  Individual
operations are combined to build multi-step queries.  Record retrieval
and formatting normally complete the process.
EDirect also provides an argument-driven function that simplifies the
extraction of data from document summaries or other results that are
returned in structured XML format.  This can eliminate the need for
writing custom software to answer ad hoc questions.  Queries can move
seamlessly between EDirect commands and UNIX utilities or scripts to
perform actions that cannot be accomplished entirely within Entrez.

Alternatives

Package Version Architecture Repository
ncbi-entrez-direct_10.9.20190219+ds-1+b10_i386.deb 10.9.20190219+ds i386 Debian Main
ncbi-entrez-direct - - -

Requires

Name Value
libc6 >= 2.3.2
libwww-perl -
libxml-simple-perl -
perl:any -

Download

Type URL
Mirror ftp.br.debian.org
Binary Package ncbi-entrez-direct_10.9.20190219+ds-1+b10_amd64.deb
Source Package ncbi-entrez-direct

Install Howto

  1. Update the package index:
    # sudo apt-get update
  2. Install ncbi-entrez-direct deb package:
    # sudo apt-get install ncbi-entrez-direct

Files

Path
/usr/bin/amino-acid-composition
/usr/bin/archive-pubmed
/usr/bin/between-two-genes
/usr/bin/download-pubmed
/usr/bin/download-sequence
/usr/bin/eaddress
/usr/bin/eblast
/usr/bin/ecitmatch
/usr/bin/econtact
/usr/bin/edirect
/usr/bin/edirutil
/usr/bin/efetch
/usr/bin/efilter
/usr/bin/einfo
/usr/bin/elink
/usr/bin/enotify
/usr/bin/entrez-phrase-search
/usr/bin/epost
/usr/bin/eproxy
/usr/bin/esearch
/usr/bin/espell
/usr/bin/esummary
/usr/bin/fetch-pubmed
/usr/bin/filter-stop-words
/usr/bin/ftp-cp
/usr/bin/ftp-ls
/usr/bin/gbf2xml
/usr/bin/index-pubmed
/usr/bin/intersect-uid-lists
/usr/bin/join-into-groups-of
/usr/bin/nquire
/usr/bin/pm-index
/usr/bin/pm-invert
/usr/bin/pm-merge
/usr/bin/pm-prepare
/usr/bin/pm-promote
/usr/bin/pm-refresh
/usr/bin/pm-stash
/usr/bin/protein-neighbors
/usr/bin/rchive
/usr/bin/reorder-columns
/usr/bin/run-ncbi-converter
/usr/bin/sort-uniq-count
/usr/bin/sort-uniq-count-rank
/usr/bin/stream-pubmed
/usr/bin/transmute
/usr/bin/word-at-a-time
/usr/bin/xtract
/usr/bin/xy-plot
/usr/share/doc/ncbi-entrez-direct/README.gz
/usr/share/doc/ncbi-entrez-direct/changelog.Debian.amd64.gz
/usr/share/doc/ncbi-entrez-direct/changelog.Debian.gz
/usr/share/doc/ncbi-entrez-direct/copyright
/usr/share/doc/ncbi-entrez-direct/examples/asp-cp
/usr/share/doc/ncbi-entrez-direct/examples/asp-ls
/usr/share/doc/ncbi-entrez-direct/examples/has-asp
/usr/share/doc/ncbi-entrez-direct/examples/test-pubmed-index
/usr/share/man/man1/amino-acid-composition.1.gz
/usr/share/man/man1/archive-pubmed.1.gz
/usr/share/man/man1/between-two-genes.1.gz
/usr/share/man/man1/download-pubmed.1.gz
/usr/share/man/man1/download-sequence.1.gz
/usr/share/man/man1/eaddress.1.gz
/usr/share/man/man1/eblast.1.gz
/usr/share/man/man1/ecitmatch.1.gz
/usr/share/man/man1/econtact.1.gz
/usr/share/man/man1/edirect.1.gz
/usr/share/man/man1/edirutil.1.gz
/usr/share/man/man1/efetch.1.gz
/usr/share/man/man1/efilter.1.gz
/usr/share/man/man1/einfo.1.gz
/usr/share/man/man1/elink.1.gz
/usr/share/man/man1/enotify.1.gz
/usr/share/man/man1/entrez-phrase-search.1.gz
/usr/share/man/man1/epost.1.gz
/usr/share/man/man1/eproxy.1.gz
/usr/share/man/man1/esearch.1.gz
/usr/share/man/man1/espell.1.gz
/usr/share/man/man1/esummary.1.gz
/usr/share/man/man1/fetch-pubmed.1.gz
/usr/share/man/man1/filter-stop-words.1.gz
/usr/share/man/man1/ftp-cp.1.gz
/usr/share/man/man1/ftp-ls.1.gz
/usr/share/man/man1/gbf2xml.1.gz
/usr/share/man/man1/index-pubmed.1.gz
/usr/share/man/man1/intersect-uid-lists.1.gz
/usr/share/man/man1/join-into-groups-of.1.gz
/usr/share/man/man1/nquire.1.gz
/usr/share/man/man1/phrase-search.1.gz
/usr/share/man/man1/pm-index.1.gz
/usr/share/man/man1/pm-invert.1.gz
/usr/share/man/man1/pm-merge.1.gz
/usr/share/man/man1/pm-prepare.1.gz
/usr/share/man/man1/pm-promote.1.gz
/usr/share/man/man1/pm-refresh.1.gz
/usr/share/man/man1/pm-stash.1.gz
/usr/share/man/man1/protein-neighbors.1.gz
/usr/share/man/man1/rchive.1.gz
/usr/share/man/man1/reorder-columns.1.gz
/usr/share/man/man1/run-ncbi-converter.1.gz
/usr/share/man/man1/sort-uniq-count-rank.1.gz
/usr/share/man/man1/sort-uniq-count.1.gz
/usr/share/man/man1/stream-pubmed.1.gz
/usr/share/man/man1/transmute.1.gz
/usr/share/man/man1/word-at-a-time.1.gz
/usr/share/man/man1/xtract.1.gz
/usr/share/man/man1/xy-plot.1.gz

Changelog

2019-02-26 - Aaron M. Ucko <ucko@debian.org>
ncbi-entrez-direct (10.9.20190219+ds-1) unstable; urgency=medium
* New upstream point release.
* debian/man/xtract.1: Update accordingly (adding -is-within).
2019-02-06 - Aaron M. Ucko <ucko@debian.org>
ncbi-entrez-direct (10.9.20190205+ds-1) unstable; urgency=medium
* New upstream release.
* debian/man/{archive-pubmed,download-pubmed,edirect,efilter,
entrez-phrase-search,esearch,espell,fetch-pubmed,index-pubmed,
phrase-search,rchive,stream-pubmed,transmute,xtract}.1: Update
accordingly.
* debian/man/{local-phrase-search,pm-{clean,current,erase,log,repack,uids,
verify}}.1: Retire per the corresponding scripts.
* debian/rules: Stop installing retired scripts local-phrase-search and
(implicitly) pm-{clean,current,erase,log,repack,uids,verify}.
2018-12-05 - Aaron M. Ucko <ucko@debian.org>
ncbi-entrez-direct (10.5.20181204+ds-2) unstable; urgency=medium
* debian/control: Actually build-depend on dh-golang.
2018-12-05 - Aaron M. Ucko <ucko@debian.org>
ncbi-entrez-direct (10.5.20181204+ds-1) unstable; urgency=medium
* New upstream release.
* (debian/).gitignore: Update per GOPATH change.
* debian/control:
- Build-depend on dh-golang, golang-github-dataence-porter2-dev,
golang-github-fatih-color-dev, golang-github-klauspost-cpuid-dev,
golang-github-rainycape-unidecode-dev, and
golang-github-shirou-gopsutil-dev.
- Set Built-Using (with the help of dh-golang).
- Bump minimum Go version to 1.10 for strings.Builder.
- Depend on libxml-simple-perl.
- Repoint Vcs-{Browser,Git} at salsa.debian.org.
- Rules-Requires-Root: no (confirmed safe).
- Standards-Version: 4.2.1 (compliant at this point).
* debian/examples: Remove local storage/indexing scripts (considered
official enough for /usr/bin at this point), leaving only asp-* and
has-asp, which promote non-free software; add test-pubmed-index.
* debian/man/{archive-pubmed,download-pubmed,download-sequence,eblast,
fetch-pubmed,index-pubmed,intersect-uid-lists,(local-)phrase-search,
pm-clean,pm-erase,pm-invert,pm-log,pm-merge,pm-prepare,pm-promote,
pm-refresh,pm-repack,pm-stash,pm-uids,pm-verify,protein-neighbors,rchive,
stream-pubmed,transmute}.1: Document newly added tools.
* debian/man/{edirect,nquire,xtract}.1: Fix old documentation bugs.
* debian/man/{efetch,efilter,elink,entrez-phrase-search,ftp-cp,ftp-ls,
nquire,xtract}.1: Update for new release.
* debian/rules:
- Change (autopopulated) GOPATH to meet dh-golang's expectations.
- Belatedly run dh --with=golang to populate (misc:)Built-Using.
- Clean up remaining cruft from when Go support was optional.
- Pull github.com/surgebase/porter2 (aka gh.c/dataence/porter2),
github.com/fatih/color (along with its dependencies
github.com/mattn/go-{colorable,isatty}), github.com/klauspost/cpuid,
github.com/rainycape/unidecode (aliased, per rchive.go's expectations,
to github.com/fiam/gounidecode/unidecode), github.com/shirou/gopsutil
(along with its dependency golang.org/x/sys/unix), and our ersatz
github.com/pbnjay/memory into the path.  (The rainycape version of
unidecode has the key advantages of being fresher and already packaged
for Debian.)
- Build rchive.go in addition to xtract.go; build both against a
common.go factored out of xtract.go.
- Install run-ncbi-converter (accidentally left off earlier).
- Flip Perl scripts back to running via /usr/bin/perl (from
/usr/bin/env perl).
- Enforce use of Go version 1.10 or newer, even if the default is older.
- Install local storage/indexing scripts to /usr/bin.  (Closes: #901028.)
- Install new eblast wrapper (corresponding to new -blast mode) and
protein-neighbors script.
* debian/vendor/github.com/pbnjay/memory/memory.go: New wrapper around
github.com/shirou/gopsutil/mem, filling in for a different third-party
library that lacks a declared license.

See Also

Package Description
ncbi-epcr_2.3.12-1-7_amd64.deb Tool to test a DNA sequence for the presence of sequence tagged sites
ncbi-rrna-data_6.1.20170106-6_all.deb large rRNA BLAST databases distributed with the NCBI toolkit
ncbi-seg_0.0.20000620-5_amd64.deb tool to mask segments of low compositional complexity in amino acid sequences
ncbi-tools-bin_6.1.20170106-6_amd64.deb NCBI libraries for biology applications (text-based utilities)
ncbi-tools-x11_6.1.20170106-6_amd64.deb NCBI libraries for biology applications (X-based utilities)
ncc_2.8-2.1+b1_amd64.deb C source code analyzer
ncdt_2.1-4_amd64.deb Display directory tree
ncdu_1.13-1+b1_amd64.deb ncurses disk usage viewer
ncftp_3.2.5-2.1_amd64.deb User-friendly and well-featured FTP client
ncl-ncarg_6.5.0-2_amd64.deb NCAR Command Language and NCAR graphics
ncl-tools_2.1.21+git20180827.c71b264-2_amd64.deb tools to deal with NEXUS files
ncmpc-lyrics_0.33-2_all.deb ncurses-based audio player (lyrics plugins)
ncmpc_0.33-2+b10_amd64.deb ncurses-based audio player
ncmpcpp_0.8.2-0.1_amd64.deb ncurses-based client for the Music Player Daemon (MPD)
nco_4.7.9-1_amd64.deb Command-line operators to analyze netCDF files
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