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Fix: kraken2 builder: update URLs #7883

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Fix: kraken2 builder: update URLs #7883

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ebdd05e
Fix: kraken2 builder: update URLs
jakobnissen Apr 13, 2026
02f5229
kraken2 builder: Fix Python compatibility
jakobnissen Apr 13, 2026
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53 changes: 49 additions & 4 deletions data_managers/data_manager_build_kraken2_database/data_manager/kraken2_build_database.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
<description>database builder</description>
<macros>
<token name="@TOOL_VERSION@">2.17.1</token>
<token name="@VERSION_SUFFIX@">0</token>
<token name="@VERSION_SUFFIX@">1</token>
<token name="@PROFILE@">24.0</token>
<xml name="common_params">
<param name="kmer_len" type="integer" value="35" label="K-mer length in BP" />
Expand Down Expand Up @@ -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' &&

Expand Down Expand Up @@ -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 + ")"])

Expand All @@ -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 $database_type.database_type == "minikraken"
Expand Down Expand Up @@ -205,8 +218,10 @@ echo '{"data_tables": {"kraken2_databases": [{"value": "$database_value", "name"
<when value="standard_prebuilt">
<conditional name="prebuilt">
<param name="prebuilt_date" type="select" label="Select index build date">
<option value="2026-02-26">February 26, 2026</option>
<option value="2025-10-15">October 15, 2025</option>
<option value="2025-07-14">July 14, 2025</option>
<option value="2025-04-02">April 2, 2025</option>
<option value="2024-12-28">December 28, 2024</option>
<option value="2024-09-04">September 4, 2024</option>
<option value="2024-06-05">June 5, 2024</option>
Expand All @@ -218,6 +233,21 @@ echo '{"data_tables": {"kraken2_databases": [{"value": "$database_value", "name"
<option value="2020-12-02">December 2, 2020</option>
<option value="2020-09-19">September 19, 2020</option>
</param>
<when value="2026-02-26">
<param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
<expand macro="viral"/>
<expand macro="minusb"/>
<expand macro="standard"/>
<expand macro="standard_08gb"/>
<expand macro="standard_16gb"/>
<expand macro="pluspf"/>
<expand macro="pluspf_08gb"/>
<expand macro="pluspf_16gb"/>
<expand macro="pluspfp"/>
<expand macro="pluspfp_08gb"/>
<expand macro="pluspfp_16gb"/>
</param>
</when>
<when value="2025-10-15">
<param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
<expand macro="viral"/>
Expand Down Expand Up @@ -248,6 +278,21 @@ echo '{"data_tables": {"kraken2_databases": [{"value": "$database_value", "name"
<expand macro="pluspfp_16gb"/>
</param>
</when>
<when value="2025-04-02">
<param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
<expand macro="viral"/>
<expand macro="minusb"/>
<expand macro="standard"/>
<expand macro="standard_08gb"/>
<expand macro="standard_16gb"/>
<expand macro="pluspf"/>
<expand macro="pluspf_08gb"/>
<expand macro="pluspf_16gb"/>
<expand macro="pluspfp"/>
<expand macro="pluspfp_08gb"/>
<expand macro="pluspfp_16gb"/>
</param>
</when>
<when value="2024-12-28">
<param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
<expand macro="viral"/>
Expand Down
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