Commit e1837425 authored by Carine Rey's avatar Carine Rey
Browse files

add a timeout at Tdg09

parent fa2f9b7f
......@@ -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
......
......@@ -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 "\"";
];
]
)
......
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