Merge pull request #6678 from astrovsky01/checkm2_pr_fix

Try adding dbkey to fix checkm2 data manager issue
galaxyproject · Jan 19, 2025 · 043f6bb · 043f6bb
2 parents 45daaec + 6a72248
commit 043f6bb
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Showing 10 changed files with 13 additions and 11 deletions.
diff --git a/data_managers/data_manager_checkm2/data_manager/checkm2_datamanager.xml b/data_managers/data_manager_checkm2/data_manager/checkm2_datamanager.xml
@@ -27,6 +27,7 @@
     "checkm2":[
       {
         "path":"uniref100.KO.1.dmnd",
+        "dbkey":"@TOOL_VERSION@",
         "name":"CheckM2 diamond DB downloaded with version @TOOL_VERSION@",
         "version":"@TOOL_VERSION@",
         "value":"@TOOL_VERSION@"

diff --git a/data_managers/data_manager_checkm2/data_manager_conf.xml b/data_managers/data_manager_checkm2/data_manager_conf.xml
@@ -3,6 +3,7 @@
         <data_table name="checkm2">
             <output>
                 <column name="value"/>
+                <column name="dbkey"/>
                 <column name="name"/>
                 <column name="version"/>
                 <column name="path" output_ref="out_file">

diff --git a/data_managers/data_manager_checkm2/test-data/checkm2.loc b/data_managers/data_manager_checkm2/test-data/checkm2.loc
@@ -1,2 +1,2 @@
 
-1.0.2	CheckM2 diamond DB downloaded with version 1.0.2	1.0.2	/tmp/tmpf_hplx2a/galaxy-dev/tool-data/checkm2/1.0.2/uniref100.KO.1.dmnd
+1.0.2   1.0.2	CheckM2 diamond DB downloaded with version 1.0.2	1.0.2	/tmp/tmpf_hplx2a/galaxy-dev/tool-data/checkm2/1.0.2/uniref100.KO.1.dmnd
diff --git a/data_managers/data_manager_checkm2/tool-data/checkm2.loc.sample b/data_managers/data_manager_checkm2/tool-data/checkm2.loc.sample
@@ -10,9 +10,9 @@
 #The checkm2_db_versioned.loc file has this format (longer white space
 #characters are TAB characters):
 #
-#<unique_build_id>	<display_name>	<version>	<file_base_path>
+#<unique_build_id>  <dbkey>  <display_name>	<version>	<file_base_path>
 
 #The <version> column indicates the checkm2 version that generated the database
 
 #
-#diamond_db_1.0.2	Diamond database	1.0.2	/mnt/galaxyIndices/Checkm2_database/uniref100.KO.1.dmnd
+#diamond_db_1.0.2   1.0.2	Diamond database	1.0.2	/mnt/galaxyIndices/Checkm2_database/uniref100.KO.1.dmnd
diff --git a/data_managers/data_manager_checkm2/tool_data_table_conf.xml.sample b/data_managers/data_manager_checkm2/tool_data_table_conf.xml.sample
@@ -1,6 +1,6 @@
 <tables>
     <table name="checkm2" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, name, version, path</columns>
+        <columns>value, dbkey, name, version, path</columns>
         <file path="tool-data/checkm2.loc" />
     </table>
 </tables>
diff --git a/data_managers/data_manager_checkm2/tool_data_table_conf.xml.test b/data_managers/data_manager_checkm2/tool_data_table_conf.xml.test
@@ -1,7 +1,7 @@
 <tables>
     <!-- Location of rnastar indexes for testing -->
     <table name="checkm2" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, name, version, path</columns>
+        <columns>value, dbkey, name, version, path</columns>
         <file path="${__HERE__}/test-data/checkm2.loc" />
     </table>
 </tables>
diff --git a/tools/checkm2/test-data/checkm2.loc b/tools/checkm2/test-data/checkm2.loc
@@ -1,3 +1,3 @@
 ##Checkm2 versioned indexes
-#build_id	display_name	path	version
-001	test_db	1.0.2	${__HERE__}/Checkm2_database/uniref100.KO.1.dmnd
+#build_id   dbkey	display_name	path	version
+001 1.0.2	test_db	1.0.2	${__HERE__}/Checkm2_database/uniref100.KO.1.dmnd
diff --git a/tools/checkm2/tool-data/checkm2.loc.sample b/tools/checkm2/tool-data/checkm2.loc.sample
@@ -10,9 +10,9 @@
 #The checkm2_db_versioned.loc file has this format (longer white space
 #characters are TAB characters):
 #
-#<unique_build_id>	<display_name>	<version>	<file_base_path>
+#<unique_build_id>  <dbkey> <display_name>	<version>	<file_base_path>
 
 #The <version> column indicates the checkm2 version that generated the database
 
 #
-#diamond_db_1.0.2	Diamond database	1.0.2	/mnt/galaxyIndices/Checkm2_database/uniref100.KO.1.dmnd
+#diamond_db_1.0.2   1.0.2	Diamond database	1.0.2	/mnt/galaxyIndices/Checkm2_database/uniref100.KO.1.dmnd
diff --git a/tools/checkm2/tool_data_table_conf.xml.sample b/tools/checkm2/tool_data_table_conf.xml.sample
@@ -1,6 +1,6 @@
 <tables>
     <table name="checkm2" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, name, version, path</columns>
+        <columns>value, dbkey, name, version, path</columns>
         <file path="tool-data/checkm2.loc" />
     </table>
 </tables>
diff --git a/tools/checkm2/tool_data_table_conf.xml.test b/tools/checkm2/tool_data_table_conf.xml.test
@@ -1,6 +1,6 @@
 <tables>
     <table name="checkm2" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, name, version, path</columns>
+        <columns>value, dbkey, name, version, path</columns>
         <file path="${__HERE__}/test-data/checkm2.loc" />
     </table>
 </tables>
Original file line number	Diff line number	Diff line change
		@@ -1,2 +1,2 @@

		1.0.2 CheckM2 diamond DB downloaded with version 1.0.2 1.0.2 /tmp/tmpf_hplx2a/galaxy-dev/tool-data/checkm2/1.0.2/uniref100.KO.1.dmnd
		1.0.2 1.0.2 CheckM2 diamond DB downloaded with version 1.0.2 1.0.2 /tmp/tmpf_hplx2a/galaxy-dev/tool-data/checkm2/1.0.2/uniref100.KO.1.dmnd