jq commands are now working

render_jbrowse2_config/commands.sh

+#!/bin/sh
+jq --argfile base default_session.json '.defaultSession = $base' config.json
+jq --argfile base tracks.json '. += $base' config.json
+
+# combined
+cat config.json | jq --argfile base default_session.json '.defaultSession = $base' | jq --argfile base tracks.json '. += $base'
\ No newline at end of file

render_jbrowse2_config/config_advanced.json → render_jbrowse2_config/tracks.json

 {
-  "aggregateTextSearchAdapters": [
-    {
-      "assemblyNames": [
-        "pdumv021"
-      ],
-      "ixFilePath": {
-        "locationType": "UriLocation",
-        "uri": "trix/pdumv021.ix"
-      },
-      "ixxFilePath": {
-        "locationType": "UriLocation",
-        "uri": "trix/pdumv021.ixx"
-      },
-      "metaFilePath": {
-        "locationType": "UriLocation",
-        "uri": "trix/pdumv021_meta.json"
-      },
-      "textSearchAdapterId": "pdumv021-index",
-      "type": "TrixTextSearchAdapter"
-    },
-    {
-      "assemblyNames": [
-        "pmassv1_masked"
-      ],
-      "ixFilePath": {
-        "locationType": "UriLocation",
-        "uri": "trix/pmassv1_masked.ix"
-      },
-      "ixxFilePath": {
-        "locationType": "UriLocation",
-        "uri": "trix/pmassv1_masked.ixx"
-      },
-      "metaFilePath": {
-        "locationType": "UriLocation",
-        "uri": "trix/pmassv1_masked_meta.json"
-      },
-      "textSearchAdapterId": "pmassv1_masked-index",
-      "type": "TrixTextSearchAdapter"
-    }
-  ],
   "tracks": [
     {
       "adapter": {