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Try adding dbkey to fix checkm2 data manager issue #6678

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merged 1 commit into from
Jan 19, 2025
Merged

Try adding dbkey to fix checkm2 data manager issue #6678

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1 change: 1 addition & 0 deletions data_managers/data_manager_checkm2/data_manager/checkm2_datamanager.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -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@"
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1 change: 1 addition & 0 deletions data_managers/data_manager_checkm2/data_manager_conf.xml
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Expand Up @@ -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">
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2 changes: 1 addition & 1 deletion data_managers/data_manager_checkm2/test-data/checkm2.loc
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@@ -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
4 changes: 2 additions & 2 deletions data_managers/data_manager_checkm2/tool-data/checkm2.loc.sample
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Expand Up @@ -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
2 changes: 1 addition & 1 deletion data_managers/data_manager_checkm2/tool_data_table_conf.xml.sample
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@@ -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>
2 changes: 1 addition & 1 deletion data_managers/data_manager_checkm2/tool_data_table_conf.xml.test
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@@ -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>
4 changes: 2 additions & 2 deletions tools/checkm2/test-data/checkm2.loc
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@@ -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
4 changes: 2 additions & 2 deletions tools/checkm2/tool-data/checkm2.loc.sample
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Expand Up @@ -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
2 changes: 1 addition & 1 deletion tools/checkm2/tool_data_table_conf.xml.sample
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@@ -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>
2 changes: 1 addition & 1 deletion tools/checkm2/tool_data_table_conf.xml.test
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Original file line number Diff line number Diff line change
@@ -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>
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