put together all docker env versions

lib/bppsuite.ml

@@ -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 ]

lib/convergence_detection.ml

@@ -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

lib/diffsel.ml

@@ -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

lib/diffsel.mli

@@ -7,7 +7,6 @@ val diffsel :
   w_every : int ->
   n_cycles: int ->
   id: int ->
-  tag: string ->
   ?seed:int ->
   unit ->
   [`diffsel] directory workflow

lib/env.ml

+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" ()
+

lib/identical.ml

@@ -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 [

lib/msd.ml

@@ -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

lib/multinomial.ml

@@ -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 [

lib/pcoc.ml

@@ -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;

lib/phyml.ml

@@ -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" [

lib/pipeline.ml

@@ -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")

lib/post_analyses.ml

@@ -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

lib/profile.ml

@@ -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

lib/ready_dataset.ml

@@ -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) ;

lib/tamuri.ml

@@ -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

lib/topological.ml

@@ -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" ];

lib/tree_dataset.ml

@@ -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) [