Docker-in-Docker (DinD) capabilities of public runners deactivated. More info

Commit 8b3cd971 authored by Carine Rey's avatar Carine Rey
Browse files

add a parsing step after diffsel

parent 003d828f
......@@ -37,22 +37,31 @@ let diffsel ~(phy_n:nucleotide_phylip workflow) ~(tree: _ workflow) ~(w_every:in
opt "-ncond" int 2 ;
opt "-x" seq [ int w_every; string " "; int n_cycles];
ident chainname ;
]
];
] in
let package = tmp // "diffsel_script_utils.py" in
let script = tmp // "diffsel_analyze_result.py" in
let chainname = (dep run_diffsel) // "myrun" in
let out = dest // "diffsel_results.tsv" in
workflow ~descr:"convergence_detection.parse_diffsel" [
docker env (
and_list [
mkdir_p dest ;
mkdir_p tmp ;
cd tmp ;
cmd "ls" [dep run_diffsel];
cmd "ls" [dep phy_n]; (* required dep to link the file in the env *)
cmd "ls" [dep tree]; (* required dep to link the file in the env *)
(*python diffsel_analyze_result.py [-r /path/to/readdiffsel] [-o output_file] chainname *)
cmd "cat" ~stdout:package [ file_dump (string Scripts.diffsel_analyze_result) ] ;
cmd "cat" ~stdout:package [ file_dump (string Scripts.diffsel_script_utils) ] ;
cmd "cat" ~stdout:script [ file_dump (string Scripts.diffsel_analyze_result) ] ;
cd tmp ;
cmd "python" [
string "diffsel_analyze_result.py" ;
opt "-r" string "_build/readdiffsel" ;
opt "-o" ident dest ;
dep (run_diffsel / selector ["myrun.chain"])
opt "-r" string "/diffsel/_build/readdiffsel" ;
opt "-o" ident out ;
ident chainname ;
]
]
)
......
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