Commit ca2ce705 authored by Carine Rey's avatar Carine Rey
Browse files

Add gene tree building using raxmlng

parent b2337639
......@@ -14,3 +14,4 @@ let env_msd = [ docker_image ~account:"carinerey" ~name:"msd" ~tag:"31082018" ()
let env_diffsel = [ docker_image ~account:"vlanore" ~name:"diffsel" ~tag:"master_a4b5" () ]
let env_raxml_ng = [ docker_image ~account:"nanozoo" ~name:"raxml-ng" ~tag:"0.9.0--435348d" () ]
......@@ -118,7 +118,8 @@ let repo_parsed_rd rd =
List.map families ~f:(fun f ->
[
Bistro_utils.Repo.item [(Family.name f) ^ ".faa"] (DP.amino_acid_alignment f);
Bistro_utils.Repo.item [(Family.name f) ^ ".nhx"] (Family.tree f);
Bistro_utils.Repo.item [(Family.name f) ^ ".species_tree.nhx"] (Family.tree f);
Bistro_utils.Repo.item [(Family.name f) ^ ".fna"] (Family.nucleotide_alignment f);
Bistro_utils.Repo.item [(Family.name f) ^ ".nw"] (DP.gene_tree f);
] |> Repo.shift (Family.name f );
) |> List.concat
......@@ -3,6 +3,7 @@ open Bistro.Shell_dsl
open Bistro
let img = Env.env_py
let img_raxml_ng = Env.env_raxml_ng
let prepare ?(descr="") tree =
Workflow.shell ~descr:("utils.parse_input_tree." ^ descr) [
......@@ -94,3 +95,18 @@ let prepare_topological_tree ?(descr="") tree =
]
] in
Workflow.select w [ "tree.topological" ]
let raxmlng_fna ?(descr="") ?(model="GTR+G") ~fna ()=
let prefix_out = dest // "out" in
let w = Workflow.shell ~descr:("raxmlng_fna." ^ descr) [
mkdir_p dest;
cmd "raxml-ng" ~img:img_raxml_ng [
opt "--msa" dep fna ;
opt "--model" string model ;
opt "--threads" int 1 ;
opt "--prefix" ident prefix_out ;
]
] in
Workflow.select w [ "out.raxml.bestTree" ]
......@@ -26,3 +26,11 @@ val prepare_tree_with_node_id :
val prepare_topological_tree :
?descr : string ->
nhx pworkflow -> topological_tree pworkflow
val raxmlng_fna :
?descr : string ->
?model : string ->
fna: nucleotide_fasta pworkflow ->
unit ->
nw pworkflow
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