rename docker image

etc/docker/ete3/Dockerfile → etc/docker/python_basics/Dockerfile

@@ -22,4 +22,6 @@ RUN apt-get update && \
 
 RUN pip install --upgrade pip 
 RUN pip install ete3==3.0.0b35
+RUN pip install scipy==0.19.1
+RUN pip install biopython==1.72
 

etc/docker/ete3/build_docker.sh → etc/docker/python_basics/build_docker.sh

@@ -2,9 +2,9 @@
 
 set -e
 
-IMAGE_NAME=ete3
+IMAGE_NAME=python_basics
 DOCKERFILE_DIR=.
-TAG=3.0.0b35
+TAG=07172018
 REPO=carinerey/$IMAGE_NAME:$TAG
 docker build -t $REPO -f ./Dockerfile $DOCKERFILE_DIR
 

lib/convergence_detection.ml

@@ -40,7 +40,7 @@ type dataset_res = {
 }
 
 let merge_results ~res_by_tools : text_file workflow =
-  let env = docker_image ~account:"carinerey" ~name:"ete3" ~tag:"3.0.0b35" () in
+  let env = docker_image ~account:"carinerey" ~name:"python_basics" ~tag:"07172018" () in
   let command = List.map res_by_tools ~f:(fun res ->
       let w = match res with
         | `Pcoc d -> Pcoc.results d
@@ -79,7 +79,6 @@ let merge_results ~res_by_tools : text_file workflow =
 
 
 let plot_merge_results ~plot_all_sites ~(res_by_tools:result list) ~tree ~faa ~tsv : svg workflow =
-  (*let env = docker_image ~account:"carinerey" ~name:"ete3" ~tag:"3.0.0b35" () in*)
   let env = docker_image ~account:"carinerey" ~name:"pcoc" ~tag:"06212018" () 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 ->

lib/tree_dataset.ml

@@ -3,7 +3,7 @@ open Bistro.EDSL
 open Bistro.Std
 open File_formats
 
-let env = docker_image ~account:"carinerey" ~name:"ete3:3.0.0b35" ()
+let env = docker_image ~account:"carinerey" ~name:"python_basics" ~tag:"07172018" ()
 
 let prepare tree =
     workflow ~descr:"utils.parse_input_tree" [