Updated tdg09 docker with fixed tdg09

etc/docker/tamuri/Dockerfile

@@ -26,9 +26,4 @@ RUN pip install docopt==0.6.2
 
 # getting tdg09
 WORKDIR /tdg09
-RUN wget https://github.com/tamuri/tdg09/archive/v1.1.2.tar.gz &&\
-    tar xzf v1.1.2.tar.gz &&\
-    rm v1.1.2.tar.gz && \
-    printf "#!/bin/bash \
-\njava -cp /tdg09/tdg09-1.1.2/dist/tdg09.jar tdg09.Analyse \$@ \
-\n" >  /usr/bin/tdg09.sh && chmod +x /usr/bin/tdg09.sh
+COPY tdg09.jar .

etc/docker/tamuri/build_docker.sh

@@ -4,7 +4,7 @@ set -e
 
 IMAGE_NAME=tdg09_python
 DOCKERFILE_DIR=.
-TAG=v1.1.2_07102018
+TAG=v1.1.2fixed.31082018
 REPO=carinerey/$IMAGE_NAME:$TAG
 docker build -t $REPO -f ./Dockerfile $DOCKERFILE_DIR
 

lib/tamuri.ml

@@ -4,7 +4,7 @@ open Bistro.EDSL
 open Bistro_bioinfo.Std
 open File_formats
 
-let env = docker_image ~account:"carinerey" ~name:"tdg09_python" ~tag:"v1.1.2_07102018" ()
+let env = docker_image ~account:"carinerey" ~name:"tdg09_python" ~tag:"v1.1.2fixed.31082018" ()
 
 let tdg09  ~(faa:aminoacid_fasta workflow) ~(tree:_ workflow) : [`tdg09] directory workflow =
   let tdg09_out = dest // "tdg09.yaml" in
@@ -30,16 +30,13 @@ let tdg09  ~(faa:aminoacid_fasta workflow) ~(tree:_ workflow) : [`tdg09] directo
         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 240;
-          string "\"java -cp /tdg09/tdg09-1.1.2/dist/tdg09.jar tdg09.Analyse";
+        cmd "java" ~stdout:tdg09_out [
+          string "-cp /tdg09/tdg09.jar tdg09.Analyse";
           opt "-tree" ident tmp_tree;
           opt "-alignment"  ident tmp_ali_phy ;
           opt "-threads"  int 1 ;
           opt "-groups"  string "XE ME" ;
-          string "\"";
-        ];
+        ]
       ]
     )
   ]