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

Commit e51ad99e authored by Carine Rey's avatar Carine Rey
Browse files

add 2 hypothesis based on different Ne, H0_BigNeInSmallNe and H0_SmallNeInBigNe

parent 0c1575dd
......@@ -46,13 +46,13 @@ let bppseqgen ?(descr="") ~nb_sites ~tree ~config : nucleotide_fasta workflow =
)
] / selector ["seq.fa"]
let conf_file_bppseqgen_multi_profiles ~tree ~profile_f ~ne_c ~config ~nb_sites_per_profile =
let conf_file_bppseqgen_multi_profiles ~tree ~profile_f ~ne_c ~ne_a ~config ~nb_sites_per_profile =
seq ~sep:"\n" (
[
assign "input.tree.file" (dep tree) ;
assign "PROFILE_F" (dep profile_f) ;
assign "number_of_sites" (int nb_sites_per_profile) ;
assign "NE_1" (int 1 ) ;
assign "NE_1" (float ne_a) ;
assign "NE_C" (float ne_c) ;
assign "NE_T" (float ne_c) ;
]
......@@ -91,7 +91,7 @@ let bppseqgen_multi_profiles_script ~config ~nb_combis ~out ~profile_f =
|}
let bppseqgen_multi_profiles ?(descr="") ~profile_f ~nb_sites ~tree ~config ~ne_c : bppseqgen_multi_profiles directory workflow =
let bppseqgen_multi_profiles ?(descr="") ~profile_f ~nb_sites ~tree ~config ~ne_c ~ne_a : bppseqgen_multi_profiles directory workflow =
let nb_sites_per_profile = 1 in
let nb_combis = Pervasives.(nb_sites / nb_sites_per_profile) in
let config_f = dest // "config.bpp" in
......@@ -102,7 +102,7 @@ let bppseqgen_multi_profiles ?(descr="") ~profile_f ~nb_sites ~tree ~config ~ne_
mkdir_p dest;
mkdir_p tmp;
cd tmp;
cmd "cat" ~stdout:config_f [(file_dump (conf_file_bppseqgen_multi_profiles ~tree ~profile_f ~config ~ne_c ~nb_sites_per_profile))];
cmd "cat" ~stdout:config_f [(file_dump (conf_file_bppseqgen_multi_profiles ~tree ~profile_f ~config ~ne_c ~ne_a ~nb_sites_per_profile))];
cmd "bash" [(file_dump (bppseqgen_multi_profiles_script ~config:config_f ~nb_combis ~out ~profile_f))];
]
)
......
......@@ -18,6 +18,7 @@ val bppseqgen_multi_profiles :
tree:nhx workflow ->
config:Bistro.Template.t list ->
ne_c: float ->
ne_a: float ->
bppseqgen_multi_profiles directory workflow
val bppseqgen_multi_profiles_get_fa :
......
......@@ -8,6 +8,8 @@ type t =
| HaPCOC
| H0_NeSmall
| H0_NeVerySmall
| H0_BigNeInSmallNe
| H0_SmallNeInBigNe
| HaPCOC_NeSmall
| HaPC_NeSmall
| H0_NeBig
......@@ -20,6 +22,8 @@ let string_of_model m = match m with
| HaPCOC -> "HaPCOC"
| H0_NeSmall -> "H0_NeSmall"
| H0_NeVerySmall -> "H0_NeVerySmall"
| H0_BigNeInSmallNe -> "H0_BigNeInSmallNe"
| H0_SmallNeInBigNe -> "H0_SmallNeInBigNe"
| HaPCOC_NeSmall -> "HaPCOC_NeSmall"
| HaPC_NeSmall -> "HaPC_NeSmall"
| H0_NeBig -> "H0_NeBig"
......@@ -86,6 +90,8 @@ let bpp_config_F nodes hyp = [
| HaPCOC -> bpp_config_HaPCOC_F
| H0_NeSmall -> bpp_config_H0_F_Ne
| H0_NeVerySmall -> bpp_config_H0_F_Ne
| H0_BigNeInSmallNe -> bpp_config_H0_F_Ne
| H0_SmallNeInBigNe -> bpp_config_H0_F_Ne
| HaPC_NeSmall -> bpp_config_HaPC_F_Ne
| HaPCOC_NeSmall -> bpp_config_HaPCOC_F_Ne
| H0_NeBig -> bpp_config_H0_F_Ne
......
......@@ -64,9 +64,16 @@ let derive_from_model ~model ~input_tree ~tree_dataset ~tree_prefix ~profile_f ~
| H0_NeBig -> 10.
| HaPC_NeBig -> 10.
| HaPCOC_NeBig -> 10.
| H0_BigNeInSmallNe -> 10.
| H0_SmallNeInBigNe -> 0.1
| _ -> 1.
in
let run_fna = Bppsuite.bppseqgen_multi_profiles ~descr ~nb_sites ~tree ~config:config_p ~profile_f ~ne_c in
let ne_a = match model with
| H0_BigNeInSmallNe -> 0.1
| H0_SmallNeInBigNe -> 10.
| _ -> 1.
in
let run_fna = Bppsuite.bppseqgen_multi_profiles ~descr ~nb_sites ~tree ~config:config_p ~profile_f ~ne_c ~ne_a in
let fna = Bppsuite.bppseqgen_multi_profiles_get_fa run_fna in
let fna_infos = Some (Bppsuite.bppseqgen_multi_profiles_get_info run_fna) in
......@@ -101,6 +108,8 @@ let derive_from_tree ~tree_dir ~tree ~profile_f ~preview ~use_concat ~ns ~no_Ne
HaPC_NeSmall ;
H0_NeBig ;
HaPC_NeBig ;
H0_BigNeInSmallNe;
H0_SmallNeInBigNe;
]
)
] |> List.concat
......
......@@ -27,6 +27,8 @@ let nodes dataset (model : Convergence_hypothesis.t) =
|H0_NeSmall -> [ "tree.H0_a.node_ids" ]
|H0_NeVerySmall -> [ "tree.H0_a.node_ids" ]
|H0_NeBig -> [ "tree.H0_a.node_ids" ]
|H0_BigNeInSmallNe-> [ "tree.H0_a.node_ids" ]
|H0_SmallNeInBigNe-> [ "tree.H0_a.node_ids" ]
)
let tree dataset mode =
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment