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Commit f4afdeb5 authored by Philippe Veber's avatar Philippe Veber
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Diffsel: remove useless id argument

parent 32f11ea6
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Showing with 3 additions and 5 deletions
lib/diffsel.ml
View file @ f4afdeb5
...@@ -50,7 +50,7 @@ echo end_it=$end_it ...@@ -50,7 +50,7 @@ echo end_it=$end_it
|} |}
let diffsel ~(phy_n:nucleotide_phylip pworkflow) ~(tree: _ pworkflow) ~(w_every:int) ~(n_cycles: int) ~(id: int) ?(descr = "") ?seed () : [`diffsel] dworkflow = let diffsel ~(phy_n:nucleotide_phylip pworkflow) ~(tree: _ pworkflow) ~(w_every:int) ~(n_cycles: int) ?(descr = "") ?seed () : [`diffsel] dworkflow =
let env = Env.env_diffsel in let env = Env.env_diffsel in
let tmp_tree = tmp // "myrun.tree" in let tmp_tree = tmp // "myrun.tree" in
let tmp_ali = tmp // "myrun.ali" in let tmp_ali = tmp // "myrun.ali" in
...@@ -65,12 +65,11 @@ let diffsel ~(phy_n:nucleotide_phylip pworkflow) ~(tree: _ pworkflow) ~(w_every: ...@@ -65,12 +65,11 @@ let diffsel ~(phy_n:nucleotide_phylip pworkflow) ~(tree: _ pworkflow) ~(w_every:
let n_cycles = if (n_cycles > 200) then 20 else n_cycles in let n_cycles = if (n_cycles > 200) then 20 else n_cycles in
let script_r = tmp // "DiffselMCMCConvergenceAnalysis.Rmd" in let script_r = tmp // "DiffselMCMCConvergenceAnalysis.Rmd" in
(*_build/diffsel -t data/samhd1.tree -d data/samhd1.ali -ncond 3 -x 1 10000 myrun*) (*_build/diffsel -t data/samhd1.tree -d data/samhd1.ali -ncond 3 -x 1 10000 myrun*)
Workflow.shell ~descr:("convergence_detection.run_diffsel." ^(string_of_int id) ^ "." ^ descr) [ Workflow.shell ~descr:("convergence_detection.run_diffsel." ^ descr) [
within_container env ( within_container env (
and_list [ and_list [
mkdir_p dest; mkdir_p dest;
cd tmp; cd tmp;
cmd "echo" [string "Run chain:"; int id];
cmd "cp" [ file_dump (string Scripts.diffselMCMCConvergenceAnalysis) ; script_r] ; cmd "cp" [ file_dump (string Scripts.diffselMCMCConvergenceAnalysis) ; script_r] ;
cmd "cp" [dep phy_n; dest_ali]; (* required dep to link the file in the env *) cmd "cp" [dep phy_n; dest_ali]; (* required dep to link the file in the env *)
cmd "cp" [dep tree; dest_tree]; (* required dep to link the file in the env *) cmd "cp" [dep tree; dest_tree]; (* required dep to link the file in the env *)
......
lib/diffsel.mli
View file @ f4afdeb5
...@@ -6,7 +6,6 @@ val diffsel : ...@@ -6,7 +6,6 @@ val diffsel :
tree:_ pworkflow -> tree:_ pworkflow ->
w_every:int -> w_every:int ->
n_cycles:int -> n_cycles:int ->
id:int ->
?descr:string -> ?descr:string ->
?seed:int -> ?seed:int ->
unit -> unit ->
......
lib/pipeline.ml
View file @ f4afdeb5
...@@ -171,7 +171,7 @@ let derive_from_det_meth ~det_meth ~(dataset : Dataset.t) ~preview = ...@@ -171,7 +171,7 @@ let derive_from_det_meth ~det_meth ~(dataset : Dataset.t) ~preview =
| `Pcoc_gamma -> `Pcoc_gamma (Pcoc.pcoc ~catx_est:10 ~plot_complete: false ~gamma:true ~faa ~tree:tree_sc) | `Pcoc_gamma -> `Pcoc_gamma (Pcoc.pcoc ~catx_est:10 ~plot_complete: false ~gamma:true ~faa ~tree:tree_sc)
| `Pcoc_C60 -> `Pcoc_C60 (Pcoc.pcoc ~catx_est:60 ~plot_complete: false ~gamma:false ~faa ~tree:tree_sc) | `Pcoc_C60 -> `Pcoc_C60 (Pcoc.pcoc ~catx_est:60 ~plot_complete: false ~gamma:false ~faa ~tree:tree_sc)
| `Tdg09 -> `Tdg09 (Tamuri.tdg09 ~faa ~tree:tree_sc) | `Tdg09 -> `Tdg09 (Tamuri.tdg09 ~faa ~tree:tree_sc)
| `Diffsel -> `Diffsel (Diffsel.diffsel ~descr ~phy_n ~tree:diffsel_tree ~w_every ~n_cycles ~id:1 ~seed ()) | `Diffsel -> `Diffsel (Diffsel.diffsel ~descr ~phy_n ~tree:diffsel_tree ~w_every ~n_cycles ~seed ())
| `Identical_LG -> `Identical_LG (Identical.identical ~faa ~tree_id ~tree_sc ~prot_model:"LG08") | `Identical_LG -> `Identical_LG (Identical.identical ~faa ~tree_id ~tree_sc ~prot_model:"LG08")
| `Identical_WAG -> `Identical_WAG (Identical.identical ~faa ~tree_id ~tree_sc ~prot_model:"WAG01") | `Identical_WAG -> `Identical_WAG (Identical.identical ~faa ~tree_id ~tree_sc ~prot_model:"WAG01")
| `Topological_LG -> `Topological_LG (Topological.topological ~faa ~tree:tree_id ~tree_conv ~prot_model:"LG08") | `Topological_LG -> `Topological_LG (Topological.topological ~faa ~tree:tree_id ~tree_conv ~prot_model:"LG08")
......
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