Unite v10

.gitignore

@@ -8,6 +8,9 @@ logs/**
 # Just in case downloads are left over
 downloads/*
 
+# Local Qiime2 tmp
+tmp/
+
 # R
 .Rhistory
 .Rapp.history

config/config.yaml

@@ -14,9 +14,9 @@ q2mod: "qiime2/2024.2"
 q2docker: "docker://quay.io/qiime2/amplicon:2024.2"
 
 # UNITE Major version listed in file names
-version: "ver9"
+version: "ver10"
 # UNITE Publication version listed in the file names
-date: "25.07.2023"
+date: "04.04.2024"
 
 # UNITE Precluster percentage
 cluster:

release_notes_newest.md

@@ -1,6 +1,6 @@
 ⚠️ This is a public demo, and has not been validated. I am not affiliated with the UNITE team.
 
-This is a classifier for [Unite v9.0](https://unite.ut.ee/repository.php) Version 18.07.2023 trained for use with [Qiime2 2024.2](https://docs.qiime2.org/2024.2/install/).
+This is a classifier for [Unite v10.0](https://unite.ut.ee/repository.php) Version 04.04.2023 trained for use with [Qiime2 2024.2](https://docs.qiime2.org/2024.2/install/).
 
 These can be used with `q2-feature-classifier` like those found on the [Data resources page](https://docs.qiime2.org/2024.2/data-resources/).
 
@@ -14,8 +14,7 @@ UNITE is licensed under CC BY-SA 4.0. If you use it, cite it! 🤝
 
 Changes:
 
-- Update Qiime2 to version 2024.2
-- This should work with any distribution (like amplicon & shotgun). If not, please [open an issue! ✅](https://github.com/colinbrislawn/unite-train/issues)
+- Update Unite to Version 10!
 
 ---
 
@@ -26,7 +25,7 @@ There are two levels of classification provided here:
 
 There are two taxa scopes:
 
-- "" Just Fungi ([I may remove this in the future, see #5](https://github.com/colinbrislawn/unite-train/issues/5))
+- "" Just Fungi
 - "all" All eukaryotes
 
 There two versions, with and without an "s":
@@ -37,14 +36,4 @@ There two versions, with and without an "s":
 
 ---
 
-Notes on dates:
-
-On the main [UNITE download page](https://unite.ut.ee/repository.php), Version number 9.0 has a Release date of 2023-07-18.
-
-However, the notes and file name say 'Version 18.07.2023' which is when it was updated ([webpage](https://doi.plutof.ut.ee/doi/10.15156/BIO/2938079), [api](https://api.plutof.ut.ee/v1/public/dois/?format=api&identifier=10.15156/BIO/2938079))
-
-I'm using the newer file.
-
----
-
 All feedback is welcome! Please [open an issue! ✅](https://github.com/colinbrislawn/unite-train/issues)

release_to_GitHub.md

@@ -16,12 +16,11 @@ gh auth login
 ## But first, spot-check one classifier
 
 ```bash
-mkdir -p /tmp/qiime2tmp
-export TMPDIR="/tmp/qiime2tmp/"
 module load qiime2
+# This makes a ./tpm/ folder in the working directory
 
 time qiime feature-classifier classify-sklearn \
-  --i-classifier results/unite_ver9_dynamic_25.07.2023-Q2-2024.2.qza \
+  --i-classifier results/unite_ver10_dynamic_04.04.2024-Q2-2024.2.qza \
   --i-reads benchmarks/dada2-single-end-rep-seqs.qza \
   --p-n-jobs 4 \
   --o-classification results/test-tax.qza
@@ -33,7 +32,8 @@ qiime taxa barplot \
   --o-visualization results/test-tax.qzv
 
 # Cleanup
-rm -rf test-tax*
+rm -f results/test-tax*
+rm -rf tmp/
 ```
 
 ## Create a new tag and release:

workflow/Snakefile

@@ -55,25 +55,25 @@ checkpoint download:  # This is not proper snakemake. I can't get my tuples to w
         """
         mkdir -p downloads
 
-        # Version 9 update. Get DOIs from here: https://unite.ut.ee/repository.php
+        # Version 10 update. Get DOIs from here: https://unite.ut.ee/repository.php
         # To get URLs you can download directly, plug them into this API:
         # https://api.plutof.ut.ee/v1/public/dois/?format=api&identifier=10.15156/BIO/2483915
 
-        # 9.0    2023-07-18    Fungi    19 051    143 384    Current    https://doi.org/10.15156/BIO/2938079
-        wget -qO- https://files.plutof.ut.ee/public/orig/FB/78/FB78E30E44793FB02E5A4D3AE18EB4A6621A2FAEB7A4E94421B8F7B65D46CA4A.tgz | \
-          tar xz -C downloads --strip-components 1 # sh_qiime_release_25.07.2023.tgz      # normal
+        # 10.0	2024-04-04	Fungi	18 895	74 190	Current	https://doi.org/10.15156/BIO/2959336
+        wget -qO- https://s3.hpc.ut.ee/plutof-public/original/db1d6ddb-a35d-48c5-8b1a-ad9dd3310c6d.tgz | \
+          tar xz -C downloads --strip-components 1
 
-        # 9.0    2023-07-18    Fungi    19 051    187 443    Current    https://doi.org/10.15156/BIO/2938080
-        wget -qO- https://files.plutof.ut.ee/public/orig/37/71/3771274B094D9CA6252DF01359756B60A2FBEEF87854CC01C2577182DBB123C7.tgz | \
-          tar xz -C downloads --strip-components 1 # sh_qiime_release_s_25.07.2023.tgz    # add s for 97% singletons
+        # 10.0	2024-04-04	Fungi	18 895	140 300	Current	https://doi.org/10.15156/BIO/2959337
+        wget -qO- https://s3.hpc.ut.ee/plutof-public/original/06daa092-e96a-48e7-9303-4402cc5c46c5.tgz | \
+          tar xz -C downloads --strip-components 1
 
-        # 9.0    2023-07-18    All eukaryotes    19 451    215 454    Current    https://doi.org/10.15156/BIO/2938081
-        wget -qO- https://files.plutof.ut.ee/public/orig/1C/C2/1CC2477429B3A703CC1C7A896A7EFF457BB0D471877CB8D18074959DBB630D10.tgz | \
-          tar xz -C downloads --strip-components 1 # sh_qiime_release_all_25.07.2023.tgz  # add all for Euks
+        # 10.0	2024-04-04	All eukaryotes	19 302	122 914	Current	https://doi.org/10.15156/BIO/2959338
+        wget -qO- https://s3.hpc.ut.ee/plutof-public/original/711a503c-589d-4138-a76f-6a8b89460ecf.tgz | \
+          tar xz -C downloads --strip-components 1
 
-        # 9.0    2023-07-18    All eukaryotes    19 451    307 276    Current    https://doi.org/10.15156/BIO/2938082
-        wget -qO- https://files.plutof.ut.ee/public/orig/7D/0C/7D0C329980D2C644CC157A8C76BBD11E78DB8B13286C98D4FEB6ECAC79D67D6F.tgz | \
-          tar xz -C downloads --strip-components 1 # sh_qiime_release_s_all_25.07.2023.tgz # and s and all for 97% Euks singletons
+        # 10.0	2024-04-04	All eukaryotes	19 302	232 937	Current	https://doi.org/10.15156/BIO/2959339
+        wget -qO- https://s3.hpc.ut.ee/plutof-public/original/55665851-81f9-4704-8287-b5971abbf85c.tgz | \
+          tar xz -C downloads --strip-components 1
 
         """