ARCHIVE-NMCDS(1)

💖 ARCHIVE-NMCDS(1) 💖

okay bestie, so this is archive-nmcds, and it lives in the NCBI Entrez Direct User's Manual. She's the girl who keeps your local RefSeq human mRNA archive cute and organized. 🧬✨

✨ 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 🌸

So like. archive-nmcds sets up a directory to be the home of a local NCBI RefSeq human mRNA archive — think of it as making the bed before the guests arrive 🛏️💅 — and then it downloads a full database dump straight from NCBI's servers. After that it organizes that whole dump into an rchive(1) trie, and it notes down the offsets of coding regions. Very demure, very mindful, very structured. 👑

💅 OPTIONS 💅

one bullet per option, no skipping, no cap:

• [-][re]index — do a full reindex, and yes it comes complete with an inverted index. the whole glow-up. ✨
• [-]clean | [-]clear — delete the Indices contents and the Increment files. decluttering era 🧹
• [-]scrub — deletes the Indices contents, the Increment files, and the Postings directories. going deeper 😭
• [-]scour — deletes the Indices contents, the Increment files, and the Postings, Data, Archive, and Sentinel directories. it's giving spring cleaning 🍓
• [-]erase — deletes the Indices contents, the Increment files, the Postings, Data, Archive, and Sentinel directories, and the Extras directory contents. full reset energy 💀
• [-]zap — deletes the entire archive. gone. not a trace. periodt. 💀✨
• -ftp — download the needed data via FTP. this is the default, bestie, so if you say nothing, you get FTP 🐟
• -http[s] — download the needed data via HTTPS. secure queen 🔒👑

🌈 ENVIRONMENT 🌈

• EDIRECT_LOCAL_ARCHIVE — the local archive directory to use. she's expected to hold an absolute path, so no sneaky relative paths, ok? 🚫
• EDIRECT_LOCAL_WORKING — the directory that holds the intermediate subtrees. also expected to hold an absolute path. when it's not set, it defaults to the local archive directory. she just moves in with her sister 🫶

👀 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).

the whole friend group fr fr 🫂💜

ngl bestie, the [-]zap option is not a vibe check you want to fail. it deletes the entire archive. read twice, run once. 😭

okay that's the whole page 💖 this one came from NCBI and it's dated 2025-05-26 — write that down, that's the tea 🍵✨ mwah, go archive something 🎀🦋