NAME

       index-pubmed - populate and index a local NCBI PubMed archive from scratch

SYNOPSIS

       index-pubmed [-collect|-index|-invert|-merge|-promote] [[-path] dir [[-temp|-work|-working] dir]]

DESCRIPTION

       index-pubmed  prepares  a  directory  to hold a local PubMed archive, then downloads a full database dump
       from NCBI's servers (along with MeSH data), organizes it into an rchive(1) trie, refreshes  and  collects
       the  versioned  records,  and  fully  indexes  the  resulting archive.  It can optionally pick up partway
       through by explicit request.

OPTIONS

       -collect
              Skip initial preparation and download, and start with forming an rchive(1) trie.

       -index Skip everything up through running rchive(1) and just perform full indexing.

       -invert
              Skip everything through the first indexing pass and start with calculating inverted indices.

       -merge Skip everything through calculating inverted indices and start with merging them.

       -promote
              Skip everything through merging inverted indices and just produce final postins files.

       [-path] dir
              Place the local archive in dir.

       [-temp|-work|-working] dir
              Place intermediate subtrees in dir.

ENVIRONMENT

       EDIRECT_PUBMED_MASTER
              Local archive directory to use in the absence of  -path.   Expected  to  hold  an  absolute  path;
              mandatory when not supplying a path on the command line.

       EDIRECT_PUBMED_WORKING
              Directory  to hold intermediate subtrees in the absence of -temp|-work|-working.  Expected to hold
              an absolute path.  Defaults to the primary local archive directory when not set.

SEE ALSO

       archive-pubmed(1),   download-ncbi-data(1),   download-pubmed(1),   expand-current(1),   fetch-pubmed(1),
       index-extras(1),  phrase-search(1), pm-collect(1), pm-index(1), pm-invert(1), pm-merge(1), pm-prepare(1),
       pm-promote(1), pm-refresh(1), pm-stash(1), rchive(1), xtract(1).

NCBI                                               2021-03-07                                    INDEX-PUBMED(1)