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

Commit b1ac3c14 authored by Carine Rey's avatar Carine Rey
Browse files

try to use local python package

parent 0f25e8c7
......@@ -27,14 +27,33 @@ let pcoc ?plot_complete ?gamma ~(faa:aminoacid_fasta workflow) ~(tree:_ workflo
let diffsel ~(phy_n:nucleotide_phylip workflow) ~(tree: _ workflow) ~(w_every:int) ~(n_cycles: int) : (*`diffsel TODO*) det_out directory workflow =
let env = docker_image ~account:"vlanore" ~name:"diffsel" ~tag:"v1.0" () in
let chainname = dest // "myrun" in
(*_build/diffsel -t data/samhd1.tree -d data/samhd1.ali -ncond 3 -x 1 10000 myrun*)
workflow ~descr:"convergence_detection.diffsel" [
let run_diffsel = workflow ~descr:"convergence_detection.run_diffsel" [
mkdir_p dest;
cmd "_build/diffsel" ~env [
opt "-t" dep tree;
opt "-d" dep phy_n ;
opt "-ncond" int 2 ;
opt "-x" seq [ int w_every; string " "; int n_cycles];
seq [ ident dest ; string "/myrun"] ;
ident chainname ;
]
] in
let package = tmp // "diffsel_script_utils.py" in
let script = tmp // "diffsel_analyze_result.py" in
workflow ~descr:"convergence_detection.parse_diffsel" [
docker env (
and_list [
(*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: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"])
]
]
)
]
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