compilation of external scripts

lib/jbuild

@@ -5,3 +5,9 @@
   (libraries (bistro.bioinfo bistro.utils))
   (preprocess (pps (ppx_jane ppx_csv_conv bistro.ppx)))
 ))
+
+(rule
+  ((targets (scripts.ml))
+     (action (run bash ocamlify_scripts.sh))
+        (deps ((file ocamlify_scripts.sh)
+	          (glob_files scripts/*)))))

lib/models_def.ml

@@ -11,9 +11,9 @@ type model =
 
 let string_of_model m = match m with
   | H0 -> "H0"
-  | Ha -> "Ha" 
+  | Ha -> "Ha"
 
-let define_bpp_config_of_model ~parsed_tree m = match m with
+let define_bpp_config_of_model m = match m with
   | H0 -> {|alphabet=Codon(letter=DNA)
              genetic_code = Standard
              input.tree.format=Nhx

lib/ocamlify_scripts.sh

+ocamlify $(for f in `ls scripts/*[^~]`; do echo --var-string $(basename ${f%.*}) $f; done | xargs) --output scripts.ml

lib/pipeline.ml

@@ -9,9 +9,9 @@ let parse_input_tree ~tree : parsed_input_tree directory workflow =
     workflow ~descr:"utils.parse_input_tree" [
     (*let env = docker_image ~account:"carinerey" ~name:"ete3:3.0.0b35" () in*)
     cmd "python" (*~env*) [
-      string "../etc/utils/bin/parse_input_tree.py";
-      opt "-t" dep tree;
-      opt "-o" ident dest;
+      file_dump (string Scripts.parse_input_tree) ;
+      opt "-t" dep tree ;
+      opt "-o" ident dest ;
     ]
   ]