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" + + + + + + + + + + + + + + +