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

Commit fb326a34 authored by Philippe Veber's avatar Philippe Veber
Browse files

Orthomam: added draw site

parent 28396f9e
......@@ -530,3 +530,22 @@ let site_ranking ?subset ~meth ~convergent_species db =
let result_files = queries ~f:detection_method in
let trees = queries ~f:(tree ~branch_length_unit:`Amino_acid) in
ranking_of_results ~alignment_ids ~convergent_species aa_alignments trees result_files ~column_label
let%pworkflow draw_site q pos =
let fasta_fn = [%path amino_acid_alignment q] in
let tree_fn = [%path tree ~branch_length_unit:`Amino_acid q] in
let convergent_species = [%eval q.convergent_species] in
let pos = [%param pos] in
let open Reviewphiltrans_toolbox in
let open Biotk_croquis in
let tree = Phylogenetics.Newick.from_file tree_fn in
let condition n = List.mem convergent_species n ~equal:String.equal in
match Biotk.Fasta.from_file fasta_fn with
| Ok (_, items) ->
let picture =
Candidate_site.make ~condition tree items pos
|> Candidate_site.draw
|> Croquis.Layout.simple
Croquis.Layout.render_pdf picture [%dest]
| Error msg -> failwith msg
......@@ -82,3 +82,5 @@ val site_ranking :
convergent_species:string list ->
Orthomam_db.t ->
Candidate_site.t list workflow
val draw_site : query -> int -> pdf file
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