Commit 631e6a6a authored by Philippe Veber's avatar Philippe Veber
Browse files

compilation of external scripts

parent d1a36d18
......@@ -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/*)))))
......@@ -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
......
ocamlify $(for f in `ls scripts/*[^~]`; do echo --var-string $(basename ${f%.*}) $f; done | xargs) --output scripts.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 ;
]
]
......
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