Docker-in-Docker (DinD) capabilities of public runners deactivated. More info

Commit f80aec39 authored by Philippe Veber's avatar Philippe Veber
Browse files

simplified multi-scripts shell steps

parent 0afb7a39
...@@ -124,24 +124,15 @@ let plot_merge_results ?t_choices ~plot_all_sites ~(res_by_tools:result list) ~t ...@@ -124,24 +124,15 @@ let plot_merge_results ?t_choices ~plot_all_sites ~(res_by_tools:result list) ~t
| Some _ -> None | Some _ -> None
| None -> Some default_t | None -> Some default_t
in in
let package_diffsel_script_utils = tmp // "diffsel_script_utils.py" in
let package_plot_data = tmp // "plot_data.py" in
let script_plot_convergent_sites = tmp // "plot_convergent_sites.py" in
let out = dest // "results.svg" in let out = dest // "results.svg" in
let inner = let inner =
Workflow.shell ~descr:"convergence_detection.plot_results" [ Workflow.shell ~descr:"convergence_detection.plot_results" [
within_container img ( within_container img (
and_list [ and_list [
mkdir_p tmp ; mkdir_p dest ;
mkdir_p dest ;
cd tmp ;
cmd "cp" [ file_dump (string Scripts.diffsel_script_utils) ; package_diffsel_script_utils ] ;
cmd "cp" [ file_dump (string Scripts.plot_data) ; package_plot_data] ;
cmd "cp" [ file_dump (string Scripts.plot_convergent_sites); script_plot_convergent_sites ] ;
cmd "python" [ cmd "python" [
string "plot_convergent_sites.py" ; Utils.script_dump Scripts.[ diffsel_script_utils ; plot_data ; plot_convergent_sites ] ;
opt "-msa" dep faa ; opt "-msa" dep faa ;
opt "-tsv" dep tsv ; opt "-tsv" dep tsv ;
opt "-tree" dep tree ; opt "-tree" dep tree ;
......
...@@ -28,9 +28,6 @@ ...@@ -28,9 +28,6 @@
# its terms. # its terms.
from ete3 import Tree, NodeStyle, TreeStyle, TextFace from ete3 import Tree, NodeStyle, TreeStyle, TextFace
from diffsel_script_utils import *
from plot_data import *
import pandas as pd import pandas as pd
from Bio import AlignIO, SeqIO, Seq, SeqRecord from Bio import AlignIO, SeqIO, Seq, SeqRecord
......
...@@ -14,3 +14,5 @@ let bash_script args code = ...@@ -14,3 +14,5 @@ let bash_script args code =
in in
seq ~sep:"\n" [ prelude ; string code ] seq ~sep:"\n" [ prelude ; string code ]
let script_dump xs =
file_dump (string (String.concat ~sep:"\n" xs))
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