From cc4db48b0027be02c4a5f4235c24e08e57882c8d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 24 Aug 2026 16:07:37 +0200
Subject: [PATCH] samestr DB builder: probe for the mOTUs db_mOTU directory

The motus_db_versioned 'path' is ambiguous: it can point at the db_mOTU
directory itself (the mOTUs DM value_translation targets
motus_database/<value>/db_mOTU, and the .loc.sample documents that) or at
its parent. The motus branch hard-coded '$path/db_mOTU/...', which only
works when path is the parent and fails otherwise (e.g. cp: can't stat
.../db_mOTU/db_mOTU_versions when path already IS the db_mOTU dir, or when
consuming a data-manager bundle where the files sit directly under path).

Adopt the same robust probe the mOTUs profiler uses
(bgruening/galaxytools#1869): normalize the dir to $path/db_mOTU when that
subdir exists, else use $path directly, then read the markers from there.
Bump to +galaxy4.
---
 .../data_manager/macros.xml                       |  2 +-
 .../data_manager/samestr_db.xml                   | 15 +++++++++------
 2 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/data_managers/data_manager_samestr_db/data_manager/macros.xml b/data_managers/data_manager_samestr_db/data_manager/macros.xml
index 12a20d221bc..c74f2657d8f 100644
--- a/data_managers/data_manager_samestr_db/data_manager/macros.xml
+++ b/data_managers/data_manager_samestr_db/data_manager/macros.xml
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.2025.111</token>
-    <token name="@VERSION_SUFFIX@">3</token>
+    <token name="@VERSION_SUFFIX@">4</token>
     <token name="@PROFILE@">25.0</token>
 
 
diff --git a/data_managers/data_manager_samestr_db/data_manager/samestr_db.xml b/data_managers/data_manager_samestr_db/data_manager/samestr_db.xml
index 1b4bfcb78ff..ad3d4f223cb 100644
--- a/data_managers/data_manager_samestr_db/data_manager/samestr_db.xml
+++ b/data_managers/data_manager_samestr_db/data_manager/samestr_db.xml
@@ -55,17 +55,20 @@
             #set $samestr_db_dir = $out_file.extra_files_path + '/samestr_db/' + $db_value
             mkdir -p '$samestr_db_dir' &&
 
-            #set $markers_info1 = $db_path + '/db_mOTU/db_mOTU_taxonomy_ref-mOTUs.tsv'
-            #set $markers_info2 = $db_path + '/db_mOTU/db_mOTU_taxonomy_meta-mOTUs.tsv'
-            #set $markers_fasta = $db_path + '/db_mOTU/db_mOTU_DB_CEN.fasta'
+            ## The motus_db_versioned 'path' may point either at the db_mOTU
+            ## directory itself (the mOTUs DM value_translation targets
+            ## motus_database/<value>/db_mOTU) or at its parent. Probe for a
+            ## nested db_mOTU/ and normalize, matching the mOTUs profiler wrapper.
+            motus_db_dir='$db_path' &&
+            if [ -d "\$motus_db_dir/db_mOTU" ]; then motus_db_dir="\$motus_db_dir/db_mOTU"; fi &&
 
             #set $db_version_file = $samestr_db_dir + '/' + $version_file_name
-            cp '$db_path'/db_mOTU/db_mOTU_versions '$db_version_file' &&
+            cp "\$motus_db_dir/db_mOTU_versions" '$db_version_file' &&
 
 
             samestr db
-            --markers-info '$markers_info1' '$markers_info2'
-            --markers-fasta '$markers_fasta'
+            --markers-info "\$motus_db_dir/db_mOTU_taxonomy_ref-mOTUs.tsv" "\$motus_db_dir/db_mOTU_taxonomy_meta-mOTUs.tsv"
+            --markers-fasta "\$motus_db_dir/db_mOTU_DB_CEN.fasta"
             --db-version '$db_version_file'
             --output-dir '$samestr_db_dir'
             &&