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Update MEDI to new DB builder and NCBI Taxonomy #39

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Update MEDI to new DB builder and NCBI Taxonomy #39

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@cdiener cdiener commented Jan 29, 2026

TODO:

  • update architeuthis
  • explain need for Kraken2 patches
  • document the new Docker image
  • provide a small example DB

cdiener and others added 30 commits March 17, 2025 14:40
@cdiener
update db script
782cc93
@cdiener
update db script
805683a
@cdiener
add the curated IDs
1d2252c
@cdiener
add the curated IDs
010b3dd
@cdiener
swich to single downloads
b407a18
@cdiener
no duplicate matches, switch to single gb downloads
ad31b08
@cdiener
fixes from cluster
9e2c458
@cdiener
fixes from cluster
7fa555d
@cdiener
several fixes
6ba1d04
local fixes
f48bd1b
@cdiener
move logs
39c9031
only download unique
1db29f9
@cdiener
fix download script
44dd942
skip problems
3465218
@cdiener
fix download
5090479
@cdiener
avoid looking for nucleotide sequences for nonredundant genera
9b8e13c
some fixes
da5b922
@cdiener
add scores beforehand
9ac0568
@cdiener
add scores beforehand
1f1e4c5
@cdiener
add scores beforehand
f536e5b
@cdiener
fix nucleoide logger
36e0d0f
@cdiener
fix nucleoide logger
2e46374
@cdiener
fix nucleoide logger
9327d03
@cdiener
add decoys
db0f1ab
@cdiener
fix decoy add
a1126a2
@cdiener
major refactor to build_kraken, now cleanly resumable
12411d9
@cdiener
major refactor to build_kraken, now cleanly resumable
08072e3
fixes to merging
5189543
@cdiener
more refactor
78a24bb
add ftp option to kraken db downloads
86af94c
cdiener added 30 commits November 4, 2025 15:15
@cdiener
remove redundant entries
16ae788
@cdiener
remove redundant entries
133d053
@cdiener
fix redundant entries
c27a185
@cdiener
fix redundant entries
0333006
@cdiener
add mem
773aaad
@cdiener
some small fixes
c9208e0
@cdiener
allow more mem for preprocessing
50ba29c
@cdiener
check for errors too
4ea06a5
@cdiener
handle insufficient reads for bracken
165561d
@cdiener
handle insufficient reads for bracken
3592df7
@cdiener
add Dockerfile
0060d61
@cdiener
add image build
3d30a26
@cdiener
see if this works
bc7c499
@cdiener
see if this works
a0884f4
@cdiener
see if this works
8fda5e0
@cdiener
see if this works
883e965
@cdiener
see if this works
a34fde0
@cdiener
see if this works
a5814aa
@cdiener
fix paths
9805439
@cdiener
add patch
7c6a011
@cdiener
add patch
2f9743d
@cdiener
add patch
d9a6a62
@cdiener
add patch
954268d
@cdiener
add patch
fb850f6
@cdiener
add patch
4a9cfeb
@cdiener
fix copy
c3ea9d6
@cdiener
change entrypoint
33ce339
@cdiener
add install script
45d98e9
@cdiener
update quant as well
90b1a84
@cdiener
Merge branch 'main' into feature/new_db
eabc1df
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@cdiener