NAME
archive-taxonomy - maintain a local NCBI taxonomy archive
SYNOPSIS
archive-taxonomy [[-]daily|[-][re]index] [[-]clean|[-]clear|[-]scrub|[-]scour|[-]erase|[-]zap] [-info] [-ftp|-http[s]]
DESCRIPTION
archive-taxonomy prepares a directory to hold a local taxonomy 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
-
Delete Indices contents and Increment files.
- [-]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-pubmed(1), download-ncbi-data(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).