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).

NCBI                                               2025-05-26                                ARCHIVE-TAXONOMY(1)