Use usher-sampled if installed (#499)

* Use the much faster usher-sampled if it is installed; otherwise, print out a message recommending that the user update usher.

pangolin/scripts/usher.smk

@@ -94,9 +94,20 @@ rule usher_inference:
         if [ -s {input.fasta:q} ]; then
             cat {input.reference:q} > {params.ref_fa:q}
             echo >> {params.ref_fa:q}
+            usher=usher
+            threads={workflow.cores}
+            if usher-sampled --help >& /dev/null; then
+                usher="usher-sampled --optimization_radius 0"
+            else
+                echo ""
+                echo "*** usher-sampled is not installed -- please upgrade usher to at least v0.6.1 ***"
+                echo "*** If you used conda to install usher, run 'conda update --no-pin usher'     ***"
+                echo "*** Alternatively if mamba is installed, run 'mamba update --no-pin usher'    ***"
+                echo ""
+            fi
             cat {input.fasta:q} >> {params.ref_fa:q}
             faToVcf -includeNoAltN {params.ref_fa:q} {params.vcf:q}
-            usher -n -D -i {input.usher_protobuf:q} -v {params.vcf:q} -T {workflow.cores} -d '{config[tempdir]}' &> {log}
+            $usher -n -D -i {input.usher_protobuf:q} -v {params.vcf:q} -T $threads -d '{config[tempdir]}' &> {log}
         else
             rm -f {output.txt:q}
             touch {output.txt:q}