diff --git a/data_managers/data_manager_build_kraken2_database/data_manager/kraken2_build_database.xml b/data_managers/data_manager_build_kraken2_database/data_manager/kraken2_build_database.xml
index 2226d29096b..6218fbf25a8 100644
--- a/data_managers/data_manager_build_kraken2_database/data_manager/kraken2_build_database.xml
+++ b/data_managers/data_manager_build_kraken2_database/data_manager/kraken2_build_database.xml
@@ -2,7 +2,7 @@
database builder
2.17.1
- 0
+ 1
24.0
@@ -56,7 +56,7 @@
#import datetime
#import re
-#set now = datetime.datetime.now(datetime.UTC).strftime("%Y-%m-%dT%H%M%SZ")
+#set now = datetime.datetime.now(datetime.timezone.utc).strftime("%Y-%m-%dT%H%M%SZ")
#set commands = []
mkdir '$out_file.extra_files_path' &&
@@ -100,6 +100,19 @@ mkdir '$out_file.extra_files_path' &&
#set display_name = amplicon_name.get(str($database_type.prebuilt.prebuilt_db)+"_"+date_url_str)
#end if
+ #set download_db = str($database_type.prebuilt.prebuilt_db)
+ #if download_db.endswith("_08gb")
+ #if date_url_str < "20220607"
+ #set download_db = download_db.replace("_08gb", "_8gb")
+ #else if date_url_str >= "20250714"
+ #set download_db = download_db.replace("_08gb", "_08_GB")
+ #end if
+ #else if download_db.endswith("_16gb")
+ #if date_url_str >= "20250714"
+ #set download_db = download_db.replace("_16gb", "_16_GB")
+ #end if
+ #end if
+
#set database_value = "_".join([now, "standard_prebuilt", str($database_type.prebuilt.prebuilt_db), str($database_type.prebuilt.prebuilt_date)])
#set database_name = " ".join(["Prebuilt Refseq indexes: ", display_name, "(Version: ", str($database_type.prebuilt.prebuilt_date), "- Downloaded:", now + ")"])
@@ -116,9 +129,9 @@ mkdir '$out_file.extra_files_path' &&
#silent commands.append("fi")
#silent commands.append("rm -rf '" + $out_file.extra_files_path + "/" + database_value + "/tmp_extract'")
#else
- #silent commands.append("wget https://genome-idx.s3.amazonaws.com/kraken/k2_" + str($database_type.prebuilt.prebuilt_db) + "_" + date_url_str + ".tar.gz")
+ #silent commands.append("wget https://genome-idx.s3.amazonaws.com/kraken/k2_" + download_db + "_" + date_url_str + ".tar.gz")
#silent commands.append("mkdir -p '" + $out_file.extra_files_path + "/" + database_value + "'")
- #silent commands.append("tar -xzf k2_" + str($database_type.prebuilt.prebuilt_db) + "_" + date_url_str + ".tar.gz -C '" + $out_file.extra_files_path + "/" + database_value + "'")
+ #silent commands.append("tar -xzf k2_" + download_db + "_" + date_url_str + ".tar.gz -C '" + $out_file.extra_files_path + "/" + database_value + "'")
#end if
#else if $database_type.database_type == "minikraken"
@@ -205,8 +218,10 @@ echo '{"data_tables": {"kraken2_databases": [{"value": "$database_value", "name"
+
+
@@ -218,6 +233,21 @@ echo '{"data_tables": {"kraken2_databases": [{"value": "$database_value", "name"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -248,6 +278,21 @@ echo '{"data_tables": {"kraken2_databases": [{"value": "$database_value", "name"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+