update pcoc version (take into account indels)

etc/docker/pcoc/Dockerfile

@@ -81,7 +81,7 @@ RUN git clone https://github.com/BioPP/bppsuite . &&\
 
 WORKDIR $HOME/pcoc
 RUN git clone https://github.com/CarineRey/pcoc.git . &&\
-    git checkout daa1b18
+    git checkout 70e60ce
 
 RUN cp -r data /data/ && \
     cp README.md /usr/local/etc/ & \

etc/docker/pcoc/build_docker.sh

@@ -4,7 +4,7 @@ set -e
 
 IMAGE_NAME=pcoc
 DOCKERFILE_DIR=.
-TAG=07022018
+TAG=08312018
 REPO=carinerey/$IMAGE_NAME:$TAG
 docker build -t $REPO -f ./Dockerfile $DOCKERFILE_DIR
 

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:"07022018" () in
+  let env = docker_image ~account:"carinerey" ~name:"pcoc" ~tag:"08312018" () in
   workflow ~descr:"convergence_detection.pcoc" [
     cmd "pcoc_det.py" ~env [
       opt "-t" dep tree;

lib/post_analyses.ml

@@ -107,7 +107,7 @@ 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:"07022018" () in
+  let env = docker_image ~account:"carinerey" ~name:"pcoc" ~tag:"08312018" () in
   workflow ~descr:("post_analyses.simu_infos." ^ descr) [
     cmd "python" ~env [
       file_dump (string Scripts.calc_simu_infos) ;

lib/topological.ml

@@ -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:"07022018" () in
+  let env = docker_image ~account:"carinerey" ~name:"pcoc" ~tag:"08312018" () in
   workflow ~descr:("topological.parse_"^prot_model) [
     mkdir dest ;
     cmd "cp" [dep bppml_out ; dest // "estimates.bppml_out.tsv" ];