Merge pull request #213 from rhysnewell/dev

Merge dev to main
rhysnewell · Sep 1, 2024 · d5f66e6 · d5f66e6
2 parents 387ac6d + 2664ca1
commit d5f66e6
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Showing 5 changed files with 8 additions and 6 deletions.
diff --git a/README.md b/README.md
@@ -136,7 +136,7 @@ use the the `aviary configure` module to update the environment variables used b
 
 These environment variables can also be configured manually, just set the following variables in your `.bashrc` file:
 ```
-export GTDBTK_DATA_PATH=/path/to/gtdb/gtdb_release207/db/ # https://gtdb.ecogenomic.org/downloads
+export GTDBTK_DATA_PATH=/path/to/gtdb/gtdb_release220/db/ # https://gtdb.ecogenomic.org/downloads
 export EGGNOG_DATA_DIR=/path/to/eggnog-mapper/2.1.8/ # https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.8#setup
 export SINGLEM_METAPACKAGE_PATH=/path/to/singlem_metapackage.smpkg/
 export CHECKM2DB=/path/to/checkm2db/

diff --git a/aviary/__init__.py b/aviary/__init__.py
@@ -1,4 +1,4 @@
-__version__ = "0.9.1"
+__version__ = "0.9.2"
 
 
 # CONSTANTS
@@ -22,4 +22,4 @@
     "r941_prom_high_g330", "r941_prom_high_g344", "r941_prom_high_g360", "r941_prom_high_g4011", "r941_prom_snp_g303", "r941_prom_snp_g322",
     "r941_prom_snp_g360", "r941_prom_sup_g507", "r941_prom_sup_snp_g507", "r941_prom_sup_variant_g507", "r941_prom_variant_g303",
     "r941_prom_variant_g322", "r941_prom_variant_g360", "r941_sup_plant_g610", "r941_sup_plant_variant_g610"
-]
+]
diff --git a/aviary/envs/checkm2.yaml b/aviary/envs/checkm2.yaml
@@ -17,5 +17,7 @@ dependencies:
   - requests
   - packaging
   - tqdm
+  - pip
+  - git
   - pip:
-      - "git+https://github.com/chklovski/CheckM2.git#egg=checkm2"
+      - "git+https://github.com/chklovski/CheckM2.git#egg=checkm2"
diff --git a/aviary/envs/gtdbtk.yaml b/aviary/envs/gtdbtk.yaml
@@ -2,5 +2,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - gtdbtk = 2.3
+  - gtdbtk = 2.4.0
   - fastani
diff --git a/aviary/modules/annotation/annotation.smk b/aviary/modules/annotation/annotation.smk
@@ -74,7 +74,7 @@ rule download_gtdb:
         'GTDBTK_DATA_PATH={params.gtdbtk_folder}; '
         'mkdir -p {params.gtdbtk_folder}; '
         # Configuration
-        'DB_URL="https://data.gtdb.ecogenomic.org/releases/latest/auxillary_files/gtdbtk_data.tar.gz"; '
+        'DB_URL="https://data.gtdb.ecogenomic.org/releases/release220/220.0/auxillary_files/gtdbtk_package/full_package/gtdbtk_r220_data.tar.gz"; '
         'TARGET_TAR_NAME="gtdbtk_data.tar.gz"; '
 
         # Script variables (no need to configure)