Update MEDI to new DB builder and NCBI Taxonomy - #39

Merged

cdiener merged 86 commits into

Gibbons-Lab:mainfrom

dienerlab:feature/new_db

Aug 4, 2026

Commits on Mar 17, 2025

update db script
cdiener
committed
782cc93
update db script
cdiener
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805683a
add the curated IDs
cdiener
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1d2252c
add the curated IDs
cdiener
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010b3dd

Commits on Mar 18, 2025

swich to single downloads
cdiener
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b407a18
no duplicate matches, switch to single gb downloads
cdiener
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ad31b08
fixes from cluster
cdiener
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9e2c458
fixes from cluster
cdiener
committed
7fa555d
several fixes
cdiener
committed
6ba1d04
local fixes
Christian Diener
committed
f48bd1b
move logs
cdiener
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39c9031
only download unique
Christian Diener
committed
1db29f9
fix download script
cdiener
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44dd942
skip problems
Christian Diener
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3465218
fix download
cdiener
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5090479

Commits on Mar 19, 2025

avoid looking for nucleotide sequences for nonredundant genera
cdiener
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9b8e13c
some fixes
Christian Diener
committed
da5b922

Commits on Mar 20, 2025

add scores beforehand
cdiener
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9ac0568
add scores beforehand
cdiener
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1f1e4c5
add scores beforehand
cdiener
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f536e5b
fix nucleoide logger
cdiener
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36e0d0f
fix nucleoide logger
cdiener
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2e46374
fix nucleoide logger
cdiener
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9327d03
add decoys
cdiener
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db0f1ab

Commits on Apr 3, 2025

fix decoy add
cdiener
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a1126a2

Commits on Apr 8, 2025

major refactor to build_kraken, now cleanly resumable
cdiener
committed
12411d9
major refactor to build_kraken, now cleanly resumable
cdiener
committed
08072e3
fixes to merging
Christian Diener
committed
5189543
more refactor
cdiener
committed
78a24bb

Commits on Apr 9, 2025

add ftp option to kraken db downloads
Christian Diener
committed
86af94c

Commits on Apr 24, 2025

further improvements to build
Christian Diener
committed
60c4a6e

Commits on May 5, 2025

make compatible with new NCBI ranks
cdiener
committed
b046ff7
several fixes to pipeline
cdiener
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30447cc
remove old prefix
cdiener
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bb0684f

Commits on Oct 31, 2025

add rsync option to database download to enable https downloads
cdiener
committed
759f56e
fix scoring
cdiener
committed
580a100

Commits on Nov 3, 2025

changes to matching and downloading
cdiener
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c98f0a6
fix match
cdiener
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52c311d
fix match
cdiener
committed
1a9bd9c
fix match
cdiener
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c448541
fix match
cdiener
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85a25d4
fix match
cdiener
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da68d5a
fix match
cdiener
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6e6a3a0
fix match
cdiener
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1acbc45

Commits on Nov 4, 2025

fix summary
cdiener
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9a825bf
fix summary
cdiener
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7bd3aa5
provide more info
cdiener
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1b85040
provide more info
cdiener
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6758c5d
provide more info
cdiener
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e532ddd
provide more info
cdiener
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4927ae0
handle missing fields in summary
cdiener
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76021d9
handle missing fields in summary
cdiener
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750ace4
remove redundant entries
cdiener
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b42f778
remove redundant entries
cdiener
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16ae788
remove redundant entries
cdiener
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133d053
fix redundant entries
cdiener
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c27a185
fix redundant entries
cdiener
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0333006
add mem
cdiener
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773aaad

Commits on Nov 17, 2025

some small fixes
cdiener
committed
c9208e0

Commits on Nov 24, 2025

allow more mem for preprocessing
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50ba29c
check for errors too
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4ea06a5
handle insufficient reads for bracken
cdiener
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165561d
handle insufficient reads for bracken
cdiener
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3592df7

Commits on Dec 2, 2025

add Dockerfile
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0060d61
add image build
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3d30a26
see if this works
cdiener
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bc7c499
see if this works
cdiener
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a0884f4
see if this works
cdiener
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8fda5e0
see if this works
cdiener
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883e965
see if this works
cdiener
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a34fde0
see if this works
cdiener
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a5814aa
fix paths
cdiener
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9805439
add patch
cdiener
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7c6a011
add patch
cdiener
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2f9743d
add patch
cdiener
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d9a6a62
add patch
cdiener
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954268d
add patch
cdiener
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fb850f6
add patch
cdiener
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4a9cfeb
fix copy
cdiener
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c3ea9d6

Commits on Dec 3, 2025

change entrypoint
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33ce339
add install script
cdiener
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45d98e9

Commits on Jan 29, 2026

update quant as well
cdiener
committed
90b1a84
Merge branch 'main' into feature/new_db
cdiener
authored
eabc1df

Commits on May 26, 2026

switch rsync to datasets CLI
cdiener
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826991d
use ftp for everything else
cdiener
committed
560e641

Commits on Aug 4, 2026

update docs
cdiener
committed
76b37e8