NAME
archive-nmcds - maintain a local NCBI RefSeq human mRNA archive
SYNOPSIS
archive-nmcds [[-][re]index] [[-]clean|[-]clear|[-]scrub|[-]scour|[-]erase|[-]zap] [-ftp|-http[s]]
DESCRIPTION
archive-nmcds prepares a directory to hold a local NCBI RefSeq human mRNA archive, then downloads a full database dump from NCBI's servers, organizes the dump into an rchive(1) trie, and notes coding regions' offsets.
OPTIONS
- [-][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.
- -ftp
-
Download needed data via FTP (default).
- -http[s]
-
Download needed data via HTTPS.
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-pids(1), archive-pmc(1), archive-pubmed(1), archive-taxonomy(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).