biology/ncbi-entrez-direct 14.9.20210423_48 FreeBSD

Access to the NCBI's suite of interconnected databases

System: FreeBSD
Repository: FreeBSD ports
Maintainer: [email protected]
Last update: 2026-10-20
Commit: d81b7ba3c3
License: PD
Categories: biology, perl5
Package size: 2060.5 KiB, 11131.2 KiB installed

Description

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.

In the other systems

The newest version among them is 14.9.20210423, as upstream numbers it.

System

Port

Version

Vulnerabilities

Status

Maintainer

Last update

FreeBSD

biology/ncbi-entrez-direct

14.9.20210423_48 newest

none known

[email protected]

2026-10-20

DragonFly

biology/ncbi-entrez-direct

14.9.20210423_25 newest

none known

[email protected]

HardenedBSD

biology/ncbi-entrez-direct

14.9.20210423_46 newest

no data

[email protected]

GhostBSD

biology/ncbi-entrez-direct

14.9.20210423_46 newest

no data

[email protected]

Install

Binary package:

pkg install ncbi-entrez-direct

From the ports tree:

cd /usr/ports/biology/ncbi-entrez-direct/ && make install clean

To depend on this port in another port's Makefile:

RUN_DEPENDS=	ncbi-entrez-direct>0:biology/ncbi-entrez-direct

Packages

The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.

Repository

aarch64

amd64

armv6

armv7

i386

FreeBSD:14:latest

14.9.20210423_47

14.9.20210423_48

14.9.20210423_30

14.9.20210423_48

FreeBSD:14:quarterly

14.9.20210423_47

14.9.20210423_48

n/a

14.9.20210423_28

14.9.20210423_48

FreeBSD:15:latest

14.9.20210423_47

14.9.20210423_48

n/a

14.9.20210423_30

FreeBSD:15:quarterly

14.9.20210423_47

14.9.20210423_48

n/a

FreeBSD:16:latest

14.9.20210423_47

14.9.20210423_48

n/a

FreeBSD:16:quarterly

n/a

Dependency graph

Ports that need it on the left, what it needs to run on the right; at most 8 of each. "Dependencies" below lists them all.

graph LR
  me["biology/ncbi-entrez-direct"]
  u0["biology/biostar-tools"] --> me
  me --> d0["archivers/brotli"]
  me --> d1["archivers/liblz4"]
  me --> d2["archivers/zstd"]
  me --> d3["converters/p5-Encode-Locale"]
  me --> d4["converters/p5-MIME-Base32"]
  me --> d5["converters/p5-MIME-Base64"]
  me --> d6["devel/libunistring"]
  me --> d7["devel/p5-Clone"]
  me -.-> dmore(["35 more"])
  classDef this fill:#ab2b28,color:#ffffff,stroke:#ab2b28
  class me this

Dependencies

As this port's Makefile names them.

Build 1

bash : shells/bash

Runtime 4

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

The full lists below include those, and their dependencies in turn.

Build dependencies 5

Run dependencies 43

Required by 1

biology/biostar-tools

Configuration

No options to configure.

USES: go:modules perl5 shebangfix
Service scripts: none
Conflicts with: ebook-tools p5-XML-Compile

Message after installing

===>   NOTICE:

The ncbi-entrez-direct port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:

https://bugs.freebsd.org/bugzilla

More information about port maintainership is available at:

https://docs.freebsd.org/en/articles/contributing/#ports-contributing

Files

pkg-plist 59

bin/accn-at-a-time
bin/align-columns
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.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/hgvs2spdi
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/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
bin/word-at-a-time
bin/xml2json
bin/xml2tbl
bin/xtract
bin/xtract.FreeBSD
bin/xy-plot

distinfo 11

File

Size

SHA256

edirect-14.9.20210423/edirect.tar.gz

829737

9d6534226164fc5dfae7abcf25bfdbd08db068b27f1c13b8a3c4681cda5b0cea

edirect-14.9.20210423/fatih-color-v1.10.0_GH0.tar.gz

1.267532e+06

a00342a7ffb8b119346dce56e152a111cbb9eab3970c429cc2ed4272aec2858e

edirect-14.9.20210423/surgebase-porter2-56e4718818e8_GH0.tar.gz

156593

d06994daa4d561c2ab477a7072bb7e40a8d39904c88ebf649a1b89105aabdf35

edirect-14.9.20210423/gedex-inflector-16278e9db813_GH0.tar.gz

6784

d872f3fb5fcc8d8ff25e915670f7ce867a035cfd7a38a2e01ef1550f8770331b

edirect-14.9.20210423/klauspost-cpuid-v1.3.1_GH0.tar.gz

367144

3bf2da7358c8ed33c05bac2ca733749ade03eadf184d81cc7b16fcbe2e230f1d

edirect-14.9.20210423/pbnjay-memory-b12e5d931931_GH0.tar.gz

3076

8903a451771edca578c2aa09848f23027dc02df2c67f675f4dd1aae257a71ad6

edirect-14.9.20210423/mattn-go-colorable-v0.1.8_GH0.tar.gz

9571

1027954f9abbe06b6e117e3047af70204dd0eb4f8c27fcd459fb2574b279755f

edirect-14.9.20210423/mattn-go-isatty-v0.0.12_GH0.tar.gz

4548

addbdc341d7685ed4cc8d2d8a8fd2bd9b784bde00d0ea99fb251039fc10c611c

edirect-14.9.20210423/fiam-gounidecode-8deddbd03fec_GH0.tar.gz

190666

b763f4eb0d0f130821b52484565b32bae1585c4cb0edc57adb94f13b67765176

edirect-14.9.20210423/golang-text-v0.3.5_GH0.tar.gz

8.348127e+06

f85d1185ba116cd40ef8cf702fe1d960ed41d039c08fd314dbeb5866f3166f27

edirect-14.9.20210423/golang-sys-v0.5.0_GH0.tar.gz

1.429723e+06

810c8f1b7704674971ab6b2b614aba20a5a1765018fd2c639f528dbbcbf88b1f

Master sites 1

ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/${PORTVERSION}/

Commit history 7

Date Commit Credits Log message

2026-10-20 d81b7ba3c3 Dag-Erling Smørgrav various: Bump Go ports for Go 1.26.10 / 1.27.3

2026-10-08 031fc6bfbf Dag-Erling Smørgrav various: Bump Go ports

2026-10-08

2414383046

Jason W. Bacon

Release numerous ports to ports@

I've been retired for a few years, and it is unlikely I will be doing any more scientific computing support in the future. I have continued to maintain ~160 ports to the best of my ability, mainly as a favor to the community, but I can no longer justify the time and effort required. I am therefore releasing most of my scientific ports, along with a few others, to ports@. I will continue to maintain ports I am actively using and those for which I am upstream.

2026-09-03 dd0905142a Adam Weinberger many: Bump go ports for 1.26.8 and 1.27.1

2026-08-19 4867821cd6 Dag-Erling Smørgrav various: Bump go ports for go-1.25.14 / 1.26.7

The latest 5 of 7 in the history this site was built from.