address comments

kbase · Aug 26, 2024 · f59a74a · f59a74a
1 parent 902c639
commit f59a74a
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Showing 3 changed files with 6 additions and 5 deletions.
diff --git a/src/loaders/compute_tools/busco/Dockerfile b/src/loaders/compute_tools/busco/Dockerfile
@@ -13,6 +13,8 @@ RUN conda config --add channels conda-forge
 ARG PYTHON_VER=3.9
 RUN conda create -n $CONDA_ENV python=$PYTHON_VER
 RUN conda install -n $CONDA_ENV pandas=2.2.2 jsonlines=4.0.0 mamba=1.5.8 pyyaml=6.0.1
+# Suggestions from BUSCO team to use mamba for speeding up the installation process:
+# https://busco.ezlab.org/busco_userguide.html#installation-with-conda
 RUN conda run -n $CONDA_ENV mamba install -c bioconda -c conda-forge -y busco=$BUSCO_VER
 
 # Activate the environment

diff --git a/src/loaders/compute_tools/busco/busco.py b/src/loaders/compute_tools/busco/busco.py
@@ -33,6 +33,8 @@ def _run_busco_single(
     version_file = os.path.join(current_dir, 'versions.yaml')
     ref_db_version = extract_latest_reference_db_version(version_file)
 
+    # Please refer to https://docs.google.com/document/d/15yV-S41Iqe20F-I2MRLWdzJwVdr8QKUfZPw7oq8WvB0/edit#heading=h.elgudks5mtxu
+    # for more information on the BUSCO command options we are using here.
     command = [
         'busco',
         '-i', str(source_file),
@@ -59,7 +61,7 @@ def _run_busco_single(
         'source_file': str(source_file),
         'data_id': data_id,
         "reference_db": {
-            "version": "odb10",
+            "version": ref_db_version,
         },
     }
     create_tool_metadata(

diff --git a/src/loaders/compute_tools/busco/versions.yaml b/src/loaders/compute_tools/busco/versions.yaml
@@ -6,7 +6,4 @@ versions:
     date: 2024-08-22
     notes: |
       - initial BUSCO implementation
-    reference_db_version: odb10
-
-#Please keep this reminder at the end of this file
-#NOTE: If the db verllsion changes, ensure the metadata information saved after running the tool in the _run_busco_single method is updated
+    reference_db_version: odb10