Commit 3d8e32a1 authored by Louis Duchemin's avatar Louis Duchemin
Browse files

RERconverge : using Rconsole module to extract results + syntax error fix

parent c39f81c7
......@@ -13,7 +13,24 @@ let marines =
let pipeline ~phenotypes =
Codepi.Orthomam.rer_converge ~db ~phenotypes ()
module Top = Bistro_utils.Toplevel_eval.Make(struct
let np = 10
let mem = 8
end)()
let result_table_script targets =
let open Codepi.R_console in
let assignments =
List.map (fun (clade, target) ->
path (Codepi.Rer_converge.string_of_clade clade) Codepi.Orthomam.(target.result_table)
) targets
in
rconsole (module Top) "library(tidyverse)" assignments
let () =
result_table_script (pipeline ~phenotypes:subterraneans)
let main () =
try
let loggers = [ Bistro_utils.Console_logger.create () ] in
let allowed_containers = [ `Docker ] in
......
......@@ -31,8 +31,7 @@ build_traits_paths <-
function(phenotypes,
gene_trees,
is_continuous,
useSpecies = NULL,
clade = c("ancestral", "terminal", "all"))
clade)
{
if (is_continuous) {
char2Paths(phenotypes, gene_trees)
......@@ -40,7 +39,6 @@ build_traits_paths <-
foreground2Tree(phenotypes,
gene_trees,
clade = clade,
# useSpecies = useSpecies,
plot=F # FIXME : plot=T raises cryptic error
) %>%
tree2Paths(gene_trees)
......@@ -54,7 +52,8 @@ results = lapply(clades, FUN=function(clade){
traits_paths <- build_traits_paths(
phenotypes,
gene_trees,
is_continuous
is_continuous,
clade
)
res <- if (is_continuous) {
......
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