NAME¶

index-extras - populate and index local BioConcepts, GeneRifs, and theme data

SYNOPSIS¶

index-extras [[-path] dir [[-temp|-work|-working] dir]]

DESCRIPTION¶

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.

OPTIONS¶

[-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¶

custom-index(1), download-ncbi-data(1), index-pubmed(1), rchive(1), theme-aliases(1), xtract(1).