correction tmp bug reprise automatique diffsel

lib/diffsel.ml

@@ -17,9 +17,11 @@ let bash_script args code =
   seq ~sep:"\n" [ prelude ; string code ]
 
 
-let diffsel_add_iterations_script ~chainname =
+let diffsel_add_iterations_script ~chainname ~ali ~tree =
   let vars = [
     "CHAIN", chainname ;
+    "ALI", ali ;
+    "TREE", tree ;
   ]
   in
   bash_script vars {|
@@ -30,12 +32,13 @@ set -e
 continue=true
 i=0
 
-while $continue 
-do
+#while $continue 
+#do
 i=$((i+1))
 echo i=$i
+ls
 # check convergence
-Rscript -e "rmarkdown::render(\"DiffselMCMCConvergenceAnalysis.Rmd\", params=list(set_trace1=\"../dest/myrun.trace\"),output_file=\"../dest/output_"$i".html\")"
+Rscript -e "rmarkdown::render(\"DiffselMCMCConvergenceAnalysis.Rmd\", params=list(set_trace1=\"../tmp/myrun_tmp.trace\"),output_file=\"../dest/output_"$i".html\")"
 new_max=`tail -n 1 new_iterations.txt | cut -f 1`
 continue=`tail -n 1 new_iterations.txt | cut -f 2`
 end_it=`tail -n 1 new_iterations.txt | cut -f 3`
@@ -44,15 +47,17 @@ echo new_max=$new_max
 echo continue=$continue
 echo end_it=$end_it
 
-if $continue
-then
-    echo "diffsel $CHAIN $new_max"
-    /diffsel/_build/diffsel $CHAIN $new_max
-fi
+#if $continue
+#then
+#    echo "diffsel $CHAIN $new_max"
+#    /diffsel/_build/diffsel $CHAIN $new_max
+#fi
+#
+#done
+#
+#cat new_iterations.txt > $CHAIN.iterations
 
-done
-
-cat new_iterations.txt > $CHAIN.iterations
+/diffsel/_build/diffsel -t $TREE -d $ALI -ncond 2 -x 1 $end_it $CHAIN
 
 |}
 
@@ -63,8 +68,9 @@ let diffsel ~(phy_n:nucleotide_phylip workflow) ~(tree: _ workflow) ~(w_every:in
   let tmp_ali = tmp // "myrun.ali" in
   let dest_tree = dest // "myrun.tree" in
   let dest_ali = dest // "myrun.ali" in
+  let chainname_tmp = tmp // "myrun_tmp" in
   let chainname = dest // "myrun" in
-  let n_cycles = if (n_cycles > 200) then 200 else n_cycles 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))  [
@@ -83,9 +89,9 @@ let diffsel ~(phy_n:nucleotide_phylip workflow) ~(tree: _ workflow) ~(w_every:in
           opt "-d" ident tmp_ali ;
           opt "-ncond"  int 2 ;
           opt "-x" seq [ int w_every; string " "; int n_cycles];
-          ident chainname ;
+          ident chainname_tmp ;
         ];
-        cmd "bash" [(file_dump (diffsel_add_iterations_script ~chainname ))];
+        cmd "bash" [(file_dump (diffsel_add_iterations_script ~chainname ~ali:tmp_ali ~tree:tmp_tree ))];
       ]
     )
   ]

lib/scripts/diffselMCMCConvergenceAnalysis.Rmd

@@ -3,7 +3,7 @@ title: "Diffsel MCMC convergence study"
 author: "Reviewphiltrans (Bastien Boussau)"
 output: html_document
 params:
-  set_trace1: "myrun.trace"
+  set_trace1: "myrun_tmp.trace"
 ---
 
 ```{r setup, include=FALSE}
@@ -24,6 +24,7 @@ trace1 = gsub(" ", "",params$set_trace1)
 ```{r, echo = T}
 library(coda)
 d1<-read.table(trace1, h=T, comment.char="&")[,1:7]
+print(d1)
 ```
 ## Summary
 
@@ -78,7 +79,8 @@ new_iterations = required_it - run_it
 
 new_iterations_bool = if (required_it > run_it) {T} else {F}
 new_iterations_bool_str = if (required_it > run_it) {"true"} else {"false"}
-new_iterations_str=paste(as.character(next_step_its), new_iterations_bool_str, required_it, sep="\t")
+new_iterations_bool_str = if (required_it > run_it) {"true"} else {"false"}
+new_iterations_str=paste(as.character(next_step_its), new_iterations_bool_str, floor(required_it * 1.2), sep="\t")
 
 if (new_iterations_bool_str) {
 write(new_iterations_str, "new_iterations.txt", append=T)