add a timeout at Tdg09

etc/docker/tamuri/Dockerfile

@@ -22,6 +22,7 @@ RUN apt-get update && \
 RUN pip install --upgrade pip 
 RUN pip install ete3==3.0.0b35
 RUN pip install biopython==1.72
+RUN pip install docopt==0.6.2
 
 # getting tdg09
 WORKDIR /tdg09

lib/tamuri.ml

@@ -11,10 +11,15 @@ let tdg09  ~(faa:aminoacid_fasta workflow) ~(tree:_ workflow) : [`tdg09] directo
   let tdg09_out = dest // "tdg09.yaml" in
   let tmp_ali_phy = dest // "tmp_ali.phy" in
   let tmp_tree = dest // "tmp.nw" in
+  let package = tmp // "diffsel_script_utils.py" in
+  let script = tmp // "try_again.py" in
   workflow ~descr:"convergence_detection.run_tdg09" [
   docker env (
       and_list [
         mkdir_p dest ;
+        mkdir_p tmp ;
+        cd tmp ;
+
         cmd "python" [
           file_dump (string Scripts.rename_input_tree_ali_tdg09) ;
           opt "-t" dep tree;
@@ -22,11 +27,19 @@ let tdg09  ~(faa:aminoacid_fasta workflow) ~(tree:_ workflow) : [`tdg09] directo
           opt "-out_a " ident tmp_ali_phy;
           opt "-out_t " ident tmp_tree;
          ];
-        cmd "tdg09.sh" ~stdout:tdg09_out [
+
+        cmd "cp"  [ file_dump (string Scripts.diffsel_script_utils) ; package] ;
+        cmd "cp" [ file_dump (string Scripts.try_again) ; script] ;
+
+        cmd "python" ~stdout:tdg09_out [
+            string "try_again.py";
+            opt "--timeout" int 60;
+            string "\"tdg09.sh";
             opt "-tree" ident tmp_tree;
             opt "-alignment"  ident tmp_ali_phy ;
             opt "-threads"  int 1 ;
             opt "-groups"  string "XE ME" ;
+            string "\"";
         ];
     ]
   )