Commit 708615e3 authored by Carine Rey's avatar Carine Rey
Browse files

put together all docker env versions

parent 98084400
......@@ -6,7 +6,7 @@ open File_formats
type bppseqgen_multi_profiles
let env = docker_image ~account:"carinerey" ~name:"bppsuite" ~tag:"07192018" ()
let env = Env.env_bppsuite
let assign k v =
seq ~sep:"=" [ string k ; v ]
......
......@@ -42,7 +42,7 @@ type dataset_res = {
}
let merge_results ?fna_infos ~res_by_tools () : text_file workflow =
let env = docker_image ~account:"carinerey" ~name:"python_basics" ~tag:"07252018" () in
let env = Env.env_py in
let fna_infos = match fna_infos with
| Some (sw) -> sw
| _ -> None
......@@ -87,7 +87,7 @@ let merge_results ?fna_infos ~res_by_tools () : text_file workflow =
]
let plot_merge_results ?t_choices ~plot_all_sites ~(res_by_tools:result list) ~tree ~faa ~tsv (): svg workflow =
let env = docker_image ~account:"carinerey" ~name:"pcoc" ~tag:"06212018" () in
let env = Env.env_pcoc in
(* use of pcoc env due to its working X server for dra plot with ete3 *)
let meths = List.map res_by_tools ~f:(fun res ->
let opt = match res with
......
......@@ -62,8 +62,8 @@ echo end_it=$end_it
|}
let diffsel ~(phy_n:nucleotide_phylip workflow) ~(tree: _ workflow) ~(w_every:int) ~(n_cycles: int) ~(id: int) ~tag ?seed () : [`diffsel] directory workflow =
let env = docker_image ~account:"vlanore" ~name:"diffsel" ~tag () in
let diffsel ~(phy_n:nucleotide_phylip workflow) ~(tree: _ workflow) ~(w_every:int) ~(n_cycles: int) ~(id: int) ?seed () : [`diffsel] directory workflow =
let env = Env.env_diffsel in
let tmp_tree = tmp // "myrun.tree" in
let tmp_ali = tmp // "myrun.ali" in
let dest_tree = dest // "myrun.tree" in
......@@ -73,7 +73,7 @@ let diffsel ~(phy_n:nucleotide_phylip workflow) ~(tree: _ workflow) ~(w_every:in
let n_cycles = if (n_cycles > 200) then 20 else n_cycles in
let script_r = tmp // "DiffselMCMCConvergenceAnalysis.Rmd" in
(*_build/diffsel -t data/samhd1.tree -d data/samhd1.ali -ncond 3 -x 1 10000 myrun*)
workflow ~descr:("convergence_detection.run_diffsel." ^ tag ^ "." ^(string_of_int id)) [
workflow ~descr:("convergence_detection.run_diffsel." ^(string_of_int id)) [
docker env (
and_list [
mkdir_p dest;
......@@ -98,7 +98,7 @@ let diffsel ~(phy_n:nucleotide_phylip workflow) ~(tree: _ workflow) ~(w_every:in
]
let check_conv run_diffsel : text_file directory workflow =
let env = docker_image ~account:"carinerey" ~name:"r_basics" ~tag:"07232018" () in
let env = Env.env_r in
let script = tmp // "DiffselMCMCConvergenceAnalysis.Rmd" in
let trace = run_diffsel / selector["myrun.trace"] in
let out = dest // "out.html" in
......@@ -124,7 +124,7 @@ let check_conv run_diffsel : text_file directory workflow =
]
let selector run_diffsel : text_file workflow =
let env = docker_image ~account:"vlanore" ~name:"diffsel" ~tag:"master_a4b5" () in
let env = Env.env_diffsel in
let package = tmp // "diffsel_script_utils.py" in
let script = tmp // "diffsel_analyze_result.py" in
let tmp_tree = tmp // "myrun.tree" in
......
......@@ -7,7 +7,6 @@ val diffsel :
w_every : int ->
n_cycles: int ->
id: int ->
tag: string ->
?seed:int ->
unit ->
[`diffsel] directory workflow
......
open Bistro.EDSL
let env_bppsuite = docker_image ~account:"carinerey" ~name:"bppsuite" ~tag:"09042018" ()
let env_pcoc = docker_image ~account:"carinerey" ~name:"pcoc" ~tag:"08312018" ()
let env_tdg09 = docker_image ~account:"carinerey" ~name:"tdg09_python" ~tag:"v1.1.2fixed.31082018" ()
let env_py = docker_image ~account:"carinerey" ~name:"python_basics" ~tag:"07252018" ()
let env_r = docker_image ~account:"carinerey" ~name:"r_basics" ~tag:"08012018" ()
let env_phyml = docker_image ~account:"carinerey" ~name:"phyml" ~tag:"v3.1" ()
let env_msd = docker_image ~account:"carinerey" ~name:"msd" ~tag:"31082018" ()
let env_diffsel = docker_image ~account:"vlanore" ~name:"diffsel" ~tag:"master_a4b5" ()
......@@ -34,7 +34,7 @@ let conf_file_bppml ~tree ~faa ~out ~config =
)
let bppml ?(descr="") ~faa ~tree ~config : _ workflow =
let env = docker_image ~account:"carinerey" ~name:"bppsuite" ~tag:"07192018" () in
let env = Env.env_bppsuite in
let config_f = dest // "config_bppml.bpp" in
let out = ident dest in
workflow ~descr:("bppsuite.bppml" ^ descr) [
......@@ -77,7 +77,7 @@ let conf_file_bppancestor ~tree ~faa ~out ~config =
)
let bppancestor ?(descr="") ~faa ~tree ~config : _ workflow =
let env = docker_image ~account:"carinerey" ~name:"bppsuite" ~tag:"07192018" () in
let env = Env.env_bppsuite in
let config_f = dest // "config_bppancestor.bpp" in
let out = ident dest in
workflow ~descr:("bppsuite.bppancestor" ^ descr) [
......@@ -98,7 +98,7 @@ let identical ~(tree_id:_ workflow) ~(tree_sc:_ workflow) ~(faa:aminoacid_fasta
let out2 = dest // "out2.tsv" in
let run_bppancestor = bppancestor ~descr:"" ~tree:tree_id ~faa ~config in
let proba = run_bppancestor / selector ["sites.tsv"] in
let env = docker_image ~account:"carinerey" ~name:"pcoc" ~tag:"07022018" () in
let env = Env.env_pcoc in
workflow ~descr:("identical."^prot_model) [
mkdir dest ;
cmd "python" ~env [
......
......@@ -4,7 +4,7 @@ open Bistro.EDSL
open Bistro_bioinfo.Std
open File_formats
let env = docker_image ~account:"carinerey" ~name:"msd" ~tag:"31082018" ()
let env = Env.env_msd
let msd ~e ~(faa:aminoacid_fasta workflow) ~(tree_sc:_ workflow) : [`msd] directory workflow =
let map_table = dest // "map.tsv" in
......
......@@ -5,7 +5,7 @@ open Bistro_bioinfo.Std
open File_formats
let multinomial ~(tree_id:_ workflow) ~(tree_sc:_ workflow) ~(faa:aminoacid_fasta workflow) : [`multinomial] directory workflow =
let env = docker_image ~account:"carinerey" ~name:"python_basics" ~tag:"07252018" () in
let env = Env.env_py in
workflow ~descr:("calc_multinomial") [
mkdir_p dest;
cmd "python" ~env [
......
......@@ -5,7 +5,7 @@ open Bistro_bioinfo.Std
open File_formats
let pcoc ?plot_complete ?gamma ?catx_est ~(faa:aminoacid_fasta workflow) ~(tree:_ workflow) : [`pcoc] directory workflow =
let env = docker_image ~account:"carinerey" ~name:"pcoc" ~tag:"08312018" () in
let env = Env.env_pcoc in
workflow ~descr:"convergence_detection.pcoc" [
cmd "pcoc_det.py" ~env [
opt "-t" dep tree;
......
......@@ -7,7 +7,7 @@ open File_formats
type phyml
let phyml ~tree phy : phyml directory workflow =
let env = docker_image ~account:"carinerey" ~name:"phyml" ~tag:"v3.1" () in
let env = Env.env_phyml in
(*mpirun -np 4 phyml -o lr -u cyp_coding.ok.nwk -i cyp_coding.phy -d 'nt' -m gtr*)
let tmp_phy = dest // "tree.phy" in
workflow ~descr:"phyml" [
......
......@@ -259,7 +259,7 @@ let derive_from_det_meth ~det_meth ~(dataset : Dataset.t) ~preview =
| `Pcoc_gamma -> `Pcoc_gamma (Pcoc.pcoc ~catx_est:10 ~plot_complete: true ~gamma:true ~faa ~tree:tree_sc)
| `Pcoc_C60 -> `Pcoc_C60 (Pcoc.pcoc ~catx_est:60 ~plot_complete: true ~gamma:false ~faa ~tree:tree_sc)
| `Tdg09 -> `Tdg09 (Tamuri.tdg09 ~faa ~tree:tree_sc)
| `Diffsel -> `Diffsel (Diffsel.diffsel ~phy_n ~tree:diffsel_tree ~w_every ~n_cycles ~id:1 ~tag:"master_a4b5" ~seed ())
| `Diffsel -> `Diffsel (Diffsel.diffsel ~phy_n ~tree:diffsel_tree ~w_every ~n_cycles ~id:1 ~seed ())
| `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")
| `Topological_LG -> `Topological_LG (Topological.topological ~faa ~tree:tree_id ~tree_conv ~prot_model:"LG08")
......
......@@ -52,9 +52,6 @@ type post_analyses_simu = {
trees_plot : text_file workflow ;
}
let r_env = docker_image ~account:"carinerey" ~name:"r_basics" ~tag:"08012018" ()
let py_env = docker_image ~account:"carinerey" ~name:"python_basics" ~tag:"07252018" ()
let is_hyp ~hyp (dataset_results :dataset_res) =
let model_prefix = dataset_results.model_prefix in
model_prefix = hyp
......@@ -74,7 +71,7 @@ let make_t_choices ?(tree_prefix="") ~haPCOC_mr
~h0_NeG5_indel_mr
~haPC_NeG5_indel_mr () : post_analyses_dir directory workflow =
let env = r_env in
let env = Env.env_r in
let out = dest // "out" in
let cmd_mr = List.map [
("--H0_NeG1" , h0_NeG1_mr );
......@@ -111,7 +108,7 @@ let make_t_choices ?(tree_prefix="") ~haPCOC_mr
]
let make_simu_infos ?(descr="") ?(fna_infos) ~faa ~tree_sc : text_file workflow =
let env = docker_image ~account:"carinerey" ~name:"pcoc" ~tag:"08312018" () in
let env = Env.env_pcoc in
workflow ~descr:("post_analyses.simu_infos." ^ descr) [
cmd "python" ~env [
file_dump (string Scripts.calc_simu_infos) ;
......@@ -123,7 +120,7 @@ let make_simu_infos ?(descr="") ?(fna_infos) ~faa ~tree_sc : text_file workflow
]
let group_simu_infos ~simu_infos_l : simu_infos directory workflow =
let env = r_env in
let env = Env.env_r in
let cmd_cp_l = List.map simu_infos_l ~f:(fun s ->
match s.simu_infos with
| Some w -> [cmd "cp" [dep w ; tmp // (s.tree_prefix ^"@"^ s.model_prefix ^ ".tsv")]]
......@@ -148,8 +145,8 @@ let group_simu_infos ~simu_infos_l : simu_infos directory workflow =
]
let plot_trees ~reinfered_tree_l : plot_trees directory workflow =
let env_r = r_env in
let env_py = py_env in
let env_r = Env.env_r in
let env_py = Env.env_py in
let cmd_cp_l = List.map reinfered_tree_l ~f:(fun rt -> [
cmd "cp" [dep rt.reinfered_tree ; tmp // (rt.tree_prefix ^"@"^ rt.model_prefix ^ ".nw")];
cmd "cp" [dep rt.input_tree ; tmp // (rt.tree_prefix ^"@input_tree.nw")]
......@@ -357,7 +354,7 @@ let post_analyses_simu_of_simu_dataset_l ~simu_dataset_l =
let plot_sens_spe_t_choices ~t_choices_l ~dataset_results_l ~profile_prefix : sens_spe_t_choices_plot directory workflow =
let env = r_env in
let env = Env.env_r in
let t_choices_dir = tmp // "t_choices_dir" in
let merged_results_dir = tmp // "merged_results_dir" in
let out = dest // "out" in
......
......@@ -9,9 +9,8 @@ type profile = {
profile_n : string;
}
let split_profile ~nb_sites ~dist_bins profile_f ~seed : text_file directory workflow =
let env = docker_image ~account:"carinerey" ~name:"python_basics" ~tag:"07252018" () in
let env = Env.env_py in
let package = tmp // "diffsel_script_utils.py" in
let script = tmp // "generate_pairs.py" in
let prefix = dest // "profile" in
......
......@@ -69,9 +69,8 @@ let paste d1 d2 =
let ready_dataset = of_raw {Raw_dataset.input_tree=r_d1.input_tree ; fna; fna_infos} in
ready_dataset
let add_indels_to_fna ~(p:float) ~(seed:int) (fna:nucleotide_fasta workflow) : nucleotide_fasta workflow =
let env = docker_image ~account:"carinerey" ~name:"python_basics" ~tag:"07252018" () in
let env = Env.env_py in
workflow ~descr:("add_indels") [
cmd "python" ~env [
file_dump (string Scripts.add_indels) ;
......
......@@ -4,7 +4,7 @@ open Bistro.EDSL
open Bistro_bioinfo.Std
open File_formats
let env = docker_image ~account:"carinerey" ~name:"tdg09_python" ~tag:"v1.1.2fixed.31082018" ()
let env = Env.env_tdg09
let tdg09 ~(faa:aminoacid_fasta workflow) ~(tree:_ workflow) : [`tdg09] directory workflow =
let tdg09_out = dest // "tdg09.yaml" in
......
......@@ -35,7 +35,7 @@ let conf_file_bppml ~tree ~faa ~out ~config =
)
let bppml ?(descr="") ~faa ~tree ~config : _ workflow =
let env = docker_image ~account:"carinerey" ~name:"bppsuite" ~tag:"07192018" () in
let env = Env.env_bppsuite in
let config_f = dest // "config_bppml.bpp" in
let out = ident dest in
workflow ~descr:("bppsuite.bppml" ^ descr) [
......@@ -59,7 +59,7 @@ let topological ~(tree:_ workflow) ~(tree_conv:_ workflow) ~(faa:aminoacid_fasta
let bppml_out = run_bppml / selector ["infos.tsv"] in
let bppml_out_conv = run_bppml_conv / selector ["infos.tsv"] in
let out = dest // "out.tsv" in
let env = docker_image ~account:"carinerey" ~name:"pcoc" ~tag:"08312018" () in
let env = Env.env_pcoc in
workflow ~descr:("topological.parse_"^prot_model) [
mkdir dest ;
cmd "cp" [dep bppml_out ; dest // "estimates.bppml_out.tsv" ];
......
......@@ -3,7 +3,7 @@ open Bistro.EDSL
open Bistro.Std
open File_formats
let env = docker_image ~account:"carinerey" ~name:"python_basics" ~tag:"07252018" ()
let env = Env.env_py
let prepare ?(descr="") tree =
workflow ~descr:("utils.parse_input_tree." ^ descr) [
......
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