diff --git a/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/VariantStorageEngineSVTest.java b/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/VariantStorageEngineSVTest.java
index 1573b27fd1..2523fad5ba 100644
--- a/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/VariantStorageEngineSVTest.java
+++ b/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/VariantStorageEngineSVTest.java
@@ -1,7 +1,7 @@
 package org.opencb.opencga.storage.core.variant;
 
+import org.junit.Assume;
 import org.junit.Before;
-import org.junit.ClassRule;
 import org.junit.Ignore;
 import org.junit.Test;
 import org.opencb.biodata.formats.variant.io.VariantReader;
@@ -25,7 +25,6 @@
 import org.opencb.opencga.storage.core.variant.query.VariantQueryResult;
 import org.opencb.opencga.storage.core.variant.query.executors.VariantQueryExecutor;
 import org.opencb.opencga.storage.core.variant.search.SearchIndexVariantQueryExecutor;
-import org.opencb.opencga.storage.core.variant.solr.VariantSolrExternalResource;
 
 import java.net.URI;
 import java.nio.file.Paths;
@@ -55,9 +54,6 @@ public abstract class VariantStorageEngineSVTest extends VariantStorageBaseTest
     protected static URI input2;
     protected static URI input3;
 
-    @ClassRule
-    public static VariantSolrExternalResource solr = new VariantSolrExternalResource();
-
     @Before
     public void before() throws Exception {
         if (!loaded) {
@@ -68,7 +64,7 @@ public void before() throws Exception {
         variantStorageEngine.getConfiguration().getCellbase().setDataRelease(ParamConstants.CELLBASE_DATA_RELEASE_GRCH38);
         variantStorageEngine.getOptions().put(VariantStorageOptions.ASSEMBLY.key(), "grch38");
         variantStorageEngine.reloadCellbaseConfiguration();
-        solr.configure(variantStorageEngine);
+
         if (!loaded) {
             loadFiles();
             loaded = true;
@@ -97,7 +93,6 @@ protected void loadFiles() throws Exception {
                 .append(VariantStorageOptions.STATS_CALCULATE.key(), true)
                 .append(VariantStorageOptions.ASSEMBLY.key(), "grch38"));
 
-        variantStorageEngine.secondaryIndex();
     }
 
     @Test
@@ -120,6 +115,7 @@ public void checkCount() throws Exception {
 
     @Test
     public void checkSecondaryAnnotationIndex() throws Exception {
+        Assume.assumeTrue(variantStorageEngine.secondaryAnnotationIndexActiveAndAlive());
         VariantQueryExecutor variantQueryExecutor = variantStorageEngine.getVariantQueryExecutor(SearchIndexVariantQueryExecutor.class);
         for (Variant variant : variantStorageEngine) {
             ParsedVariantQuery query = variantStorageEngine
diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/test/java/org/opencb/opencga/storage/hadoop/variant/HadoopVariantStorageEngineSVTest.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/test/java/org/opencb/opencga/storage/hadoop/variant/HadoopVariantStorageEngineSVTest.java
index fbcbd77347..26bcb49bb0 100644
--- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/test/java/org/opencb/opencga/storage/hadoop/variant/HadoopVariantStorageEngineSVTest.java
+++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/test/java/org/opencb/opencga/storage/hadoop/variant/HadoopVariantStorageEngineSVTest.java
@@ -1,8 +1,6 @@
 package org.opencb.opencga.storage.hadoop.variant;
 
-import org.junit.Assert;
-import org.junit.ClassRule;
-import org.junit.Test;
+import org.junit.*;
 import org.junit.experimental.categories.Category;
 import org.opencb.biodata.models.variant.StudyEntry;
 import org.opencb.biodata.models.variant.Variant;
@@ -12,13 +10,15 @@
 import org.opencb.opencga.storage.core.variant.adaptors.GenotypeClass;
 import org.opencb.opencga.storage.core.variant.adaptors.VariantQuery;
 import org.opencb.opencga.storage.core.variant.query.VariantQueryResult;
+import org.opencb.opencga.storage.core.variant.solr.VariantSolrExternalResource;
+import org.opencb.opencga.storage.hadoop.HBaseCompat;
 import org.opencb.opencga.storage.hadoop.variant.adaptors.VariantHadoopDBAdaptor;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import java.util.*;
 
-import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.*;
 import static org.opencb.opencga.core.api.ParamConstants.OVERWRITE;
 
 /**
@@ -33,9 +33,46 @@ public class HadoopVariantStorageEngineSVTest extends VariantStorageEngineSVTest
     public static HadoopExternalResource externalResource = new HadoopExternalResource();
     private Logger logger = LoggerFactory.getLogger(getClass());
 
+    public static VariantSolrExternalResource solr = new VariantSolrExternalResource();
+
+    @BeforeClass
+    public static void beforeClass() throws Exception {
+        if (HBaseCompat.getInstance().isSolrTestingAvailable()) {
+            solr.before();
+            solr.configure(externalResource.getVariantStorageEngine());
+            System.out.println("Start embedded solr");
+        } else {
+            System.out.println("Skip embedded solr tests");
+        }
+    }
+
+    @AfterClass
+    public static void afterClass() throws Exception {
+        if (HBaseCompat.getInstance().isSolrTestingAvailable()) {
+            solr.after();
+        }
+    }
+
+    @Override
+    public void before() throws Exception {
+        super.before();
+        if (HBaseCompat.getInstance().isSolrTestingAvailable()) {
+            solr.configure(variantStorageEngine);
+        }
+    }
+
     @Override
     protected void loadFiles() throws Exception {
+        if (HBaseCompat.getInstance().isSolrTestingAvailable()) {
+            solr.configure(variantStorageEngine);
+        }
         super.loadFiles();
+        if (HBaseCompat.getInstance().isSolrTestingAvailable()) {
+            variantStorageEngine.secondaryIndex();
+            assertTrue(variantStorageEngine.secondaryAnnotationIndexActiveAndAlive());
+        } else {
+            assertFalse(variantStorageEngine.secondaryAnnotationIndexActiveAndAlive());
+        }
         VariantHbaseTestUtils.printVariants(getVariantStorageEngine().getDBAdaptor(), newOutputUri(getTestName().getMethodName()));
     }