Add cmdstan

src/bfx_tools/cmdstan.ml

@@ -0,0 +1,75 @@
+(* Wraps make from cmdstan, i.e. compiles a .stan file *)
+
+open Biokepi_run_environment
+open Common
+
+(*let run_program = Machine.run_program biokepi_machine*)
+
+let compile_model ~stan_model ~(run_with : Machine.t) =
+  let open KEDSL in
+  let cmdstan = Machine.get_tool run_with Machine.Tool.Default.cmdstan in
+  workflow_node (single_file ~host:Machine.(as_host run_with) stan_model)
+  ~name:"Compile .stan file"
+  ~edges: [
+    depends_on Machine.Tool.(ensure cmdstan);
+  ]
+  ~make:(Machine.run_program run_with
+           Program.(
+             Machine.Tool.init cmdstan
+             (* && shf "cd %s" cmdstan_dir *)
+             && shf "make %s" stan_model
+           )
+        )
+
+let fit_model ~stan_model ~fit_method
+    ~data_file
+    ~output_file
+    ~(run_with : Machine.t) =
+  let open KEDSL in (* when is this necessary? *)
+  workflow_node
+    (single_file output_file ~host:(Machine.as_host run_with))
+    ~name:(sprintf "Fitting %s" stan_model)
+    ~make:(
+      Machine.run_program run_with
+        Program.(
+          shf "%s \
+              %s \
+              data file=%s \
+              output file=%s" stan_model fit_method data_file output_file
+        )
+    )
+    ~edges:[
+      depends_on (compile_model ~stan_model:stan_model ~run_with);
+    ]
+
+let stan_summary_node ~model_output_csv ~summary_csv
+  ~(run_with : Machine.t)
+  =
+  let open KEDSL in
+  let cmdstan = Machine.get_tool run_with Machine.Tool.Default.cmdstan in
+  workflow_node (single_file summary_csv ~host:(Machine.as_host run_with))
+    ~name:("stansummary " ^ model_output_csv ^ " to " ^ summary_csv)
+    ~edges: [
+      depends_on Machine.Tool.(ensure cmdstan);
+    ]
+    ~make:(Machine.run_program run_with
+             Program.(
+               Machine.Tool.init cmdstan
+               && shf "bin/stansummary %s --csv_file=%s" model_output_csv summary_csv
+             )
+          )
+
+(* sticking the simplest possible Configuration in here for now *)
+module Configuration = struct
+
+  type t = {
+    name: string;
+    parameters: (string * string) list
+  }
+
+  let default = {
+    name = "default";
+    parameters = []
+  }
+
+end

src/environment_setup/tool_providers.ml

@@ -180,6 +180,17 @@ end
 
 let add_to_dollar_path ~path = KEDSL.Program.shf "export PATH=%s:$PATH" path
 
+let make_and_copy_dir dir =
+  fun ~path -> KEDSL.Program.(
+      shf "echo %s" path
+      && sh "make"
+      && sh "cd .."
+      && shf "cp -r %s %s" dir path)
+let make_and_copy_contents =
+  fun ~path -> KEDSL.Program.(
+      shf "echo %s" path
+      && sh "make build"
+      && shf "cp -r * %s" path)
 let make_and_copy_bin bin =
   fun ~path -> KEDSL.Program.(
       sh "make" && shf "cp %s %s" bin path)
@@ -192,6 +203,14 @@ let witness_list l =
     KEDSL.list_of_files ~host (List.map l ~f:(fun bin -> path // bin))
     |> fun p -> object method is_done = p#is_done end
 
+let cmdstan =
+  Installable_tool.make
+    Machine.Tool.Default.cmdstan
+    ~url:"https://github.com/stan-dev/cmdstan/releases/download/v2.15.0/cmdstan-2.15.0.zip"
+    ~install_program:(make_and_copy_contents)
+    ~init_program:(fun ~path -> KEDSL.Program.(shf "cd %s" path))
+    ~witness:(witness_file "bin/stanc")
+
 let bwa =
   Installable_tool.make
     Machine.Tool.Default.bwa
@@ -508,10 +527,7 @@ let fastqc =
       ~init_program:add_to_dollar_path
       ~witness:(witness_file binary)
 
-let default_tool_location
-    msg
-    (): Workflow_utilities.Download.tool_file_location
-  =
+let default_tool_location msg (): Workflow_utilities.Download.tool_file_location =
   `Fail (sprintf "No location provided for %s" msg)
 
 let default_netmhc_config () = Netmhc.(
@@ -562,6 +578,7 @@ let default_toolkit
       install samblaster;
       install_git freebayes;
       install delly2;
+      install cmdstan;
     ];
     Biopam.default ~run_program ~host
       ~install_path:(install_tools_path // "biopam-kit") ();

src/run_environment/machine.ml

@@ -72,6 +72,7 @@ module Tool = struct
     let topiary = create "topiary" ~version:"1.2.1"
     let vaxrank = create "vaxrank" ~version:"0.6.0"
     let isovar = create "isovar" ~version:"0.7.0"
+    let cmdstan = create "cmdstan" ~version:"2.15.0"
   end
 
   type t = {