Bugfix to JBrowseSessionTransform

Author: bbimber

SequenceAnalysis/pipeline_code/extra_tools_install.sh

@@ -305,3 +305,16 @@ then
 else
     echo "Already installed"
 fi
+
+if [[ ! -e ${LKTOOLS_DIR}/bbmap || ! -z $FORCE_REINSTALL ]];
+then
+    echo "Cleaning up previous installs"
+    rm -Rf $LKTOOLS_DIR/bbmap
+
+    wget https://sourceforge.net/projects/bbmap/files/BBMap_39.25.tar.gz
+    tar -xf BBMap_39.25.tar.gz
+
+    mv bbmap $LKTOOLS_DIR/
+else
+    echo "Already installed"
+fi

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/MosaikWrapper.java

@@ -58,7 +58,7 @@ public MosaikWrapper(@Nullable Logger logger)
 
     public static class MosaikAlignmentStep extends AbstractAlignmentPipelineStep<MosaikWrapper> implements AlignmentStep
     {
-        public MosaikAlignmentStep(AlignmentStepProvider provider, PipelineContext ctx)
+        public MosaikAlignmentStep(AlignmentStepProvider<?> provider, PipelineContext ctx)
         {
             super(provider, ctx, new MosaikWrapper(ctx.getLogger()));
         }