update r_basics docker version (add pandoc)

etc/docker/r_basics/Dockerfile

@@ -4,3 +4,7 @@ MAINTAINER Carine Rey carine.rey@ens-lyon.org
 
 RUN echo 'install.packages(c("optparse", "ggplot2", "reshape2", "cowplot", "coda"), repos="https://mirror.ibcp.fr/pub/CRAN/", dependencies=TRUE)' > /tmp/packages.R \
 && Rscript /tmp/packages.R
+
+RUN apt-get update && \
+    apt-get install --no-install-recommends -qy \
+    pandoc

etc/docker/r_basics/build_docker.sh

@@ -4,7 +4,7 @@ set -e
 
 IMAGE_NAME=r_basics
 DOCKERFILE_DIR=.
-TAG=07162018
+TAG=07232018
 REPO=carinerey/$IMAGE_NAME:$TAG
 docker build -t $REPO -f ./Dockerfile $DOCKERFILE_DIR
 

lib/diffsel.ml

@@ -32,7 +32,7 @@ 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:"07162018" () in
+  let env = docker_image ~account:"carinerey" ~name:"r_basics" ~tag:"07232018" () in
   let script = tmp // "DiffselMCMCConvergenceAnalysis.Rmd" in
   let trace = run_diffsel / selector["myrun.trace"] in
   let out = dest // "out.html" in

lib/post_analyses.ml

@@ -40,13 +40,14 @@ type post_analyses_simu = {
   simu_infos_plot : text_file workflow ;
 }
 
+let r_env = docker_image ~account:"carinerey" ~name:"r_basics" ~tag:"07232018" ()
 
 let is_hyp ~hyp (dataset_results :dataset_res) =
   let model_prefix = dataset_results.model_prefix in
   model_prefix = hyp
 
 let make_t_choices ~h0_merged_results ~ha_merged_results : post_analyses_dir directory workflow =
-  let env = docker_image ~account:"carinerey" ~name:"r_basics" ~tag:"07162018" () in
+  let env = r_env in
   let out = dest // "out" in
   workflow ~descr:"post_analyses.t_choices" [
     docker env (
@@ -74,7 +75,7 @@ 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 = docker_image ~account:"carinerey" ~name:"r_basics" ~tag:"07162018" () in
+  let env = r_env 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")]]
@@ -163,7 +164,7 @@ let post_analyses_simu_of_simu_dataset_l ~simu_dataset_l =
 
 
 let plot_sens_spe_t_choices ~t_choices_l ~dataset_results_l ~profile : sens_spe_t_choices_plot directory workflow =
-  let env = docker_image ~account:"carinerey" ~name:"r_basics" ~tag:"07162018" () in
+  let env = r_env in
   let t_choices_dir = tmp // "t_choices_dir" in
   let merged_results_dir = tmp // "merged_results_dir" in
   let out = dest // "out" in