Commit 9443ef17 authored by LANORE Vincent's avatar LANORE Vincent
Browse files

Updated tdg09 docker with fixed tdg09

parent 9e81940a
......@@ -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 .
......@@ -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
......
......@@ -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 "\"";
];
]
]
)
]
......
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