index-extras - populate and index local BioConcepts, GeneRifs, and theme data
index-extras [[
-path]
dir [[
-temp|
-work|
-working]
dir]]
index-extras prepares a directory to hold local BioConcepts, GeneRifs,
and Percha-Altman theme data, then downloads full dumps from NCBI and Zenodo
servers, organizes the data into an
rchive(1) trie, and fully indexes
the resulting archive.
- [-path] dir
- Place the local archive in dir.
- [-temp|-work|-working] dir
- Place intermediate subtrees in dir.
- 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.
custom-index(1),
download-ncbi-data(1),
index-pubmed(1),
rchive(1),
theme-aliases(1),
xtract(1).