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 = ...@@ -13,7 +13,24 @@ let marines =
let pipeline ~phenotypes = let pipeline ~phenotypes =
Codepi.Orthomam.rer_converge ~db ~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 () = let () =
result_table_script (pipeline ~phenotypes:subterraneans)
let main () =
try try
let loggers = [ Bistro_utils.Console_logger.create () ] in let loggers = [ Bistro_utils.Console_logger.create () ] in
let allowed_containers = [ `Docker ] in let allowed_containers = [ `Docker ] in
......
...@@ -31,8 +31,7 @@ build_traits_paths <- ...@@ -31,8 +31,7 @@ build_traits_paths <-
function(phenotypes, function(phenotypes,
gene_trees, gene_trees,
is_continuous, is_continuous,
useSpecies = NULL, clade)
clade = c("ancestral", "terminal", "all"))
{ {
if (is_continuous) { if (is_continuous) {
char2Paths(phenotypes, gene_trees) char2Paths(phenotypes, gene_trees)
...@@ -40,7 +39,6 @@ build_traits_paths <- ...@@ -40,7 +39,6 @@ build_traits_paths <-
foreground2Tree(phenotypes, foreground2Tree(phenotypes,
gene_trees, gene_trees,
clade = clade, clade = clade,
# useSpecies = useSpecies,
plot=F # FIXME : plot=T raises cryptic error plot=F # FIXME : plot=T raises cryptic error
) %>% ) %>%
tree2Paths(gene_trees) tree2Paths(gene_trees)
...@@ -54,7 +52,8 @@ results = lapply(clades, FUN=function(clade){ ...@@ -54,7 +52,8 @@ results = lapply(clades, FUN=function(clade){
traits_paths <- build_traits_paths( traits_paths <- build_traits_paths(
phenotypes, phenotypes,
gene_trees, gene_trees,
is_continuous is_continuous,
clade
) )
res <- if (is_continuous) { res <- if (is_continuous) {
......
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