Add Kraken2 2.17.2 and prebuilt Kraken2 databases

ansible/roles/compiled/tasks/bio/kraken2.yaml

@@ -51,3 +51,89 @@
             src: kraken2.lua
             dest: "{{ kraken2_module_dir }}/{{ version_number }}.lua"
             mode: u=rw,g=r,o=r
+
+# NOTE: this file is included once per Kraken2 version, so the databases are
+# checked once per version too; the stat guard makes repeat passes no-ops.
+- name: Install Kraken2 databases
+  vars:
+    kraken2_db_root: "{{ bio_data_dir }}/kraken2"
+  tags:
+    - never
+    - kraken2-db
+  block:
+    - name: Ensure Kraken2 database root exists
+      ansible.builtin.file:
+        path: "{{ kraken2_db_root }}"
+        state: directory
+        mode: u=rwx,g=rwx,o=rx
+
+    - name: Check which Kraken2 databases are already installed
+      ansible.builtin.stat:
+        path: "{{ kraken2_db_root }}/{{ database.name }}/INSTALLED.ansible"
+      loop: "{{ kraken2_databases }}"
+      loop_control:
+        loop_var: database
+        label: "{{ database.name }}"
+      register: kraken2_db_status
+
+    - name: Install missing Kraken2 database
+      vars:
+        missing_databases: "{{ kraken2_db_status.results | rejectattr('stat.exists') | map(attribute='database') | list }}"
+      block:
+        - name: Create Kraken2 database dir
+          ansible.builtin.file:
+            path: "{{ kraken2_db_root }}/{{ database.name }}"
+            state: directory
+            mode: u=rwx,g=rwx,o=rx
+          loop: "{{ missing_databases }}"
+          loop_control:
+            loop_var: database
+            label: "{{ database.name }}"
+
+        - name: Download Kraken2 database
+          ansible.builtin.get_url:
+            url: "{{ database.url }}"
+            dest: "{{ kraken2_db_root }}/{{ database.url | basename }}"
+            checksum: "{{ database.checksum }}"
+            mode: u=rw,g=r,o=r
+            timeout: 60
+            # Stage beside dest, not in remote_tmp (~/.ansible/tmp): home is quota-limited
+            # and the final move is then a same-filesystem rename, not an 80 GB copy
+            tmp_dest: "{{ kraken2_db_root }}"
+          loop: "{{ missing_databases }}"
+          loop_control:
+            loop_var: database
+            label: "{{ database.name }}"
+
+        # NOTE: tar rather than ansible.builtin.unarchive, which decompresses the
+        # archive a second time just to list it — slow at ~80 GB for Standard.
+        - name: Extract Kraken2 database
+          ansible.builtin.command:
+            cmd: >-
+              tar -xzf {{ kraken2_db_root }}/{{ database.url | basename }}
+              --strip-components={{ database.strip_components | default(0) }}
+              --no-same-owner
+              -C {{ kraken2_db_root }}/{{ database.name }}
+          loop: "{{ missing_databases }}"
+          loop_control:
+            loop_var: database
+            label: "{{ database.name }}"
+
+        - name: Mark Kraken2 database as installed
+          ansible.builtin.file:
+            path: "{{ kraken2_db_root }}/{{ database.name }}/INSTALLED.ansible"
+            state: touch
+            mode: u=rw,g=r,o=r
+          loop: "{{ missing_databases }}"
+          loop_control:
+            loop_var: database
+            label: "{{ database.name }}"
+
+        - name: Remove Kraken2 database archive
+          ansible.builtin.file:
+            path: "{{ kraken2_db_root }}/{{ database.url | basename }}"
+            state: absent
+          loop: "{{ missing_databases }}"
+          loop_control:
+            loop_var: database
+            label: "{{ database.name }}"

ansible/roles/compiled/tasks/bio/main.yml

@@ -705,6 +705,42 @@
       - version_number: "2.1.3"
         url: "https://github.com/DerrickWood/kraken2/archive/refs/tags/v2.1.3.tar.gz"
         checksum: "sha512:2365cdcff3d955bcb83bb2cd942c9f22757b80ed568b187835cfb9d0516973b652a6fa8c8ff3ebadbd2c78c125046fd74434524281c29e77a09397103a293835"
+      # NOTE: upstream dropped the "v" prefix from tags from 2.17.2 onwards
+      - version_number: "2.17.2"
+        url: "https://github.com/DerrickWood/kraken2/archive/refs/tags/2.17.2.tar.gz"
+        checksum: "sha512:b1a3bc8a1f55991c33bbcc22f5ba8f7bdc46b7428d53a1321be18ccd1150ae0a22269a84a65e37a3c6ddd9c21265b0a49b56b9c113b17aa6115ea1534ec4ba87"
+    # Prebuilt indexes from https://benlangmead.github.io/aws-indexes/k2, installed with
+    # -t kraken2,kraken2-db. md5 checksums are upstream's (<collection>.md5); EuPathDB and
+    # the 16S sets publish none, so their sha256 was computed locally.
+    kraken2_databases:
+      - name: "16S_Greengenes13.5_20200326"
+        url: "https://genome-idx.s3.amazonaws.com/kraken/16S_Greengenes13.5_20200326.tgz"
+        checksum: "sha256:cbf0b477b39a03b4781ee0130fcf9592b97917e88d5bbbfc5e15f1aec0183e9e"
+        strip_components: 1
+      - name: "16S_Silva138_20200326"
+        url: "https://genome-idx.s3.amazonaws.com/kraken/16S_Silva138_20200326.tgz"
+        checksum: "sha256:edc7dcf6e1b73d7c665413bfa3be609b11f651b557e49ea5b857ddf89edc604f"
+        strip_components: 1
+      - name: "16S_Silva132_20200326"
+        url: "https://genome-idx.s3.amazonaws.com/kraken/16S_Silva132_20200326.tgz"
+        checksum: "sha256:c2ac6488fd063c2adf75985d6c824b3fd0553ee28d6ef7e7ac1a975f543226e9"
+        strip_components: 1
+      - name: "16S_RDP11.5_20200326"
+        url: "https://genome-idx.s3.amazonaws.com/kraken/16S_RDP11.5_20200326.tgz"
+        checksum: "sha256:0f6d294be2b14f846d80c60634e7bb7b9cc922490e9ccab368551956813d6dc6"
+        strip_components: 1
+      - name: "viral_20260626"
+        url: "https://genome-idx.s3.amazonaws.com/kraken/k2_viral_20260626.tar.gz"
+        checksum: "md5:2eecc5fe6eef12cb23b524996bfb7d08"
+      - name: "minusb_20260626"
+        url: "https://genome-idx.s3.amazonaws.com/kraken/k2_minusb_20260626.tar.gz"
+        checksum: "md5:ac49723ccb0d1c1c55ab98ca9abf75c1"
+      - name: "eupathdb48_20230407"
+        url: "https://genome-idx.s3.amazonaws.com/kraken/k2_eupathdb48_20230407.tar.gz"
+        checksum: "sha256:ff3eb2b2d71d05182167ac238167885e3dec4b26cd44244fbb061b97718aa9d3"
+      - name: "standard_20260626"
+        url: "https://genome-idx.s3.amazonaws.com/kraken/k2_standard_20260626.tar.gz"
+        checksum: "md5:70477acf5ad91271725d77aadd8ca6b1"
   ansible.builtin.include_tasks:
     file: "kraken2.yaml"
   loop: "{{ versions }}"

ansible/roles/compiled/templates/kraken2.lua

@@ -7,3 +7,4 @@ whatis("Keywords: Kraken2")
 whatis("Description: Kraken2 {{ version_number }}")
 
 prepend_path('PATH', '{{ install_dir }}')
+setenv('KRAKEN2_DB_PATH', '{{ bio_data_dir }}/kraken2')