Man page - archive-pubmed(1)
Packages contains this manual
- join-into-groups-of(1)
- gbf2ref(1)
- quote-grouped-elements(1)
- disambiguate-nucleotides(1)
- gff-sort(1)
- pma2pme(1)
- pm-collect(1)
- pm-setup(1)
- systematic-mutations(1)
- sort-uniq-count-rank(1)
- archive-pids(1)
- efetch(1)
- pma2apa(1)
- gbf2fsa(1)
- intersect-uid-lists(1)
- skip-if-file-exists(1)
- archive-taxonomy(1)
- jsonl2xml(1)
- efetch.ncbi(1)
- difference-uid-lists(1)
- download-ncbi-data(1)
- snp2tbl(1)
- einfo(1)
- gbf2facds(1)
- tbl2prod(1)
- cit2pmid(1)
- run-ncbi-converter(1)
- args2slice(1)
- xy-plot(1)
- xml2tbl(1)
- archive-nihocc(1)
- fsa2xml(1)
- download-pubmed(1)
- just-top-hits(1)
- sort-uniq-count(1)
- sort-by-length(1)
- json2xml(1)
- filter-stop-words(1)
- archive-nmcds(1)
- print-missing-subranges(1)
- word-at-a-time(1)
- between-two-genes(1)
- esearch(1)
- xfilter(1)
- einfo.ncbi(1)
- efilter(1)
- gbf2info(1)
- pmc2bioc(1)
- download-ncbi-software(1)
- filter-columns(1)
- pm-refresh(1)
- edict(1)
- split-at-intron(1)
- amino-acid-composition(1)
- expand-current(1)
- gbf2xml(1)
- gff2xml(1)
- find-in-gene(1)
- archive-pmc(1)
- download-sequence(1)
- snp2hgvs(1)
- pmc2info(1)
- download-pmc(1)
- bsmp2info(1)
- pm-clean(1)
- esample(1)
- gene2range(1)
- print-columns(1)
- scn2xml(1)
- xfetch(1)
- archive-pubmed(1)
- ds2pme(1)
- tbl2xml(1)
- xml2fsa(1)
- xlink(1)
- download-flatfile(1)
- reorder-columns(1)
- blst2tkns(1)
- exclude-uid-lists(1)
- sort-table(1)
- fuse-segments(1)
- transmute(1)
- combine-uid-lists(1)
- pair-at-a-time(1)
- spdi2tbl(1)
- ecollect(1)
- accn-at-a-time(1)
- custom-index(1)
- gbf2tbl(1)
- align-columns(1)
- asn2ref(1)
- pm-prepare(1)
- elink(1)
- archive-nlmnlp(1)
- xtract(1)
- gm2segs(1)
- epost(1)
- hgvs2spdi(1)
- esummary(1)
- rchive(1)
- refseq-nm-cds(1)
- ini2xml(1)
- xinfo(1)
- xsearch(1)
- csv2xml(1)
- uniq-table(1)
- yaml2xml(1)
- ref2pmid(1)
- filter-record(1)
- fuse-ranges(1)
- nquire(1)
- filter-genbank(1)
apt-get install ncbi-entrez-direct
Manual
ARCHIVE-PUBMED
NAMESYNOPSIS
DESCRIPTION
OPTIONS
ENVIRONMENT
SEE ALSO
NAME
archive-pubmed - maintain a local NCBI PubMed archive
SYNOPSIS
archive-pubmed [[ - ] download ] [[ - ] verify ] [[ - ] missing ] [[ - ] daily | [ - ][ re ] index ] [[ - ] stem [ med ]] [[ - ] clean |[ - ] clear |[ - ] scrap |[ - ] scrub | [ - ] scour |[ - ] erase |[ - ] zap ] [ -info ] [ -ftp | -http [ s ]]
DESCRIPTION
archive-pubmed prepares a directory to hold a local PubMed archive, then downloads a full database dump and auxiliary vocabulary data from NCBI’s servers, organizes the dump into an rchive (1) trie, and refreshes the versioned records.
OPTIONS
[ - ] download
Download the dump but perform no further processing.
[ - ] verify
Verify that all downloaded files are in good shape.
[ - ] missing
Check for missing downloads.
[ - ] daily
Additionally produce or update an inverted index.
[ - ][ re ] index
Fully reindex, complete with an inverted index.
[ - ] clean |[ - ] clear
Delete Indices contents and Increment files.
[ - ] scrap
Delete Postings directories.
[ - ] scrub
Delete Indices contents, Increment files, and Postings directories.
[ - ] scour
Delete Indices contents, Increment files, and Postings , Data , Archive , and Sentinel directories.
[ - ] erase
Delete Indices contents, Increment files, Postings , Data , Archive , and Sentinel directories, and Extras directory contents.
|
[ - ] zap |
Delete entire archive. |
||
|
-info |
Check whether the archive is complete and up to date; report what’s wrong if it isn’t. |
||
|
-ftp |
Download needed data via FTP (default). |
-http [ s ]
Download needed data via HTTPS.
[ -path ] dir
Place the local archive in dir .
[ -temp | -work [ ing ]] dir
Place intermediate subtrees in dir .
ENVIRONMENT
EDIRECT_LOCAL_ARCHIVE
Local archive directory to use; expected to hold an absolute path.
EDIRECT_LOCAL_WORKING
Directory to hold intermediate subtrees; expected to hold an absolute path. Defaults to the local archive directory when not set.
SEE ALSO
archive-nihocc (1), archive-nlmnlp (1), archive-nmcds (1), archive-pids (1), archive-pmc (1), archive-taxonomy (1), cit2pmid (1), custom-index (1), download-ncbi-data (1), download-pubmed (1), edict (1), expand-current (1), nquire (1), pm-clean (1), pm-collect (1), pm-prepare (1), pm-refresh (1), pm-setup (1), rchive (1), ref2pmid (1), xfetch (1), xfilter (1), xinfo (1), xlink (1), xsearch (1). xtract (1).