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

Commit 99b996a3 authored by Carine Rey's avatar Carine Rey
Browse files

add H0+Ha

parent 875124f2
......@@ -146,3 +146,12 @@ let fa2phy ~(fna: nucleotide_fasta workflow) : nucleotide_phylip workflow =
assign "param" (file_dump (conf_file_bppseqman_fa2phy ~fna)) ;
]
]
let paste_fna ~(fna_l: nucleotide_fasta workflow list) : nucleotide_fasta workflow =
workflow ~descr:"bppsuite.catfasta" [
cmd "catfasta2phyml.pl" ~stdout:dest ~env (List.concat [
[string "-f" ] ;
List.map fna_l ~f:(fun fna -> dep fna) ;
])
]
......@@ -25,3 +25,7 @@ val fna2faa :
val fa2phy :
fna: nucleotide_fasta workflow ->
nucleotide_phylip workflow
val paste_fna:
fna_l: nucleotide_fasta workflow list ->
nucleotide_fasta workflow
......@@ -43,9 +43,15 @@ let derive_from_tree ~tree_dir ~tree ~profile_f ~preview =
H0NeBig ;
HaNeBig ;
] in
List.map models ~f:(fun model ->
derive_from_model ~model ~tree ~tree_dataset ~tree_prefix ~profile_f ~preview
)
let hypos = List.map models ~f:(fun model ->
derive_from_model ~model ~tree ~tree_dataset ~tree_prefix ~profile_f ~preview
) in
let ready_dataset_H0 = (derive_from_model ~model:H0 ~tree ~tree_dataset ~tree_prefix ~profile_f ~preview).dataset in
let ready_dataset_Ha = (derive_from_model ~model:Ha ~tree ~tree_dataset ~tree_prefix ~profile_f ~preview).dataset in
let hypos_concat =
[{ Dataset.model_prefix="H0+Ha"; tree_prefix; dataset = Ready_dataset.paste ready_dataset_H0 ready_dataset_Ha};]
in
List.concat [ hypos ; hypos_concat ]
let derive_sim ~tree_dir ~trees ~profile_fn ~preview =
let profile_f = input profile_fn in
......
......@@ -33,3 +33,10 @@ let repo rd =
let to_raw { input_tree ; fna } =
{ Raw_dataset.input_tree ; fna }
let paste d1 d2 =
let r_d1 = to_raw d1 in
let r_d2 = to_raw d2 in
let fna = Bppsuite.paste_fna [r_d1.fna ; r_d2.fna ] in
let ready_dataset = of_raw {Raw_dataset.input_tree=r_d1.input_tree ; fna} in
ready_dataset
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