NAME
archive-nlmnlp - maintain a local BioConcepts (PubTator) and GeneRifs archive
SYNOPSIS
archive-nlmnlp [[-]daily|[-][re]index] [[-]clean|[-]clear|[-]scrub|[-]scour|[-]scratch|[-]erase] [-ftp|-http[s]]
DESCRIPTION
archive-nlmnlp prepares a directory to hold a local BioConcepts (PubTator) and GeneRifs archive, then downloads a full database dump from NCBI's servers, organizes the dump into an rchive(1) trie, and refreshes the versioned records.
OPTIONS
- [-]daily
-
Additionally produce or update an inverted index.
- [-][re]index
-
Fully reindex, complete with an inverted index.
- [-]clean|[-]clear|[-]scrub|[-]scour|[-]scratch|[-]erase
-
Delete Scratch directories.
- -ftp
-
Download needed data via FTP (default).
- -http[s]
-
Download needed data via HTTPS.
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-nmcds(1), archive-pids(1), archive-pmc(1), archive-pubmed(1), archive-taxonomy(1), nquire(1), pm-clean(1), pm-prepare(1), pm-setup(1), rchive(1), xfetch(1), xfilter(1), xinfo(1), xlink(1), xsearch(1), xtract(1).