Merge pull request #38 from TurakhiaLab/updated_lastz_install

Updated LASTZ installation

Author: ang037

roadies_env.sh

@@ -62,6 +62,18 @@ if [ ! -d "workflow/scripts/sampling/build" ]; then
     cd ../../../..
 fi
 
+# Download and setup LASTZ if not already done
+if [ ! -d "workflow/scripts/lastz_32" ]; then
+    cd workflow/scripts
+    wget https://github.com/lastz/lastz/archive/refs/heads/master.zip
+    unzip master.zip
+    cd lastz-master/src/
+    make lastz_32 flagsFor32="-Dmax_sequence_index=63 -Dmax_malloc_index=40 -Ddiag_hash_size=4194304"
+    make install_32
+    cp lastz_32 ../../
+    cd ../../../../
+fi
+
 # Install ete3 for the user, only if it is not already installed
 python3 -m pip show ete3 &>/dev/null || python3 -m pip install --user ete3
 

workflow/rules/mashtree.smk

@@ -76,6 +76,7 @@ rule lastz:
 	params:
 		species = "{sample}",
 		identity = config['IDENTITY'],
+		identity_deep = config['IDENTITY_DEEP'],
 		coverage = config['COVERAGE'],
 		continuity = config['CONTINUITY'],
 		align_dir = config['OUT_DIR']+ "/alignments",