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Docker-in-Docker (DinD) capabilities of public runners deactivated.
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VEBER Philippe
codepi
Commits
e1837425
Commit
e1837425
authored
Jul 10, 2018
by
Carine Rey
Browse files
add a timeout at Tdg09
parent
fa2f9b7f
Changes
2
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2 changed files
with
15 additions
and
1 deletion
+15
-1
etc/docker/tamuri/Dockerfile
etc/docker/tamuri/Dockerfile
+1
-0
lib/tamuri.ml
lib/tamuri.ml
+14
-1
No files found.
etc/docker/tamuri/Dockerfile
View file @
e1837425
...
...
@@ -22,6 +22,7 @@ RUN apt-get update && \
RUN
pip
install
--upgrade
pip
RUN
pip
install
ete3
==
3.0.0b35
RUN
pip
install
biopython
==
1.72
RUN
pip
install
docopt
==
0.6.2
# getting tdg09
WORKDIR
/tdg09
...
...
lib/tamuri.ml
View file @
e1837425
...
...
@@ -11,10 +11,15 @@ let tdg09 ~(faa:aminoacid_fasta workflow) ~(tree:_ workflow) : [`tdg09] directo
let
tdg09_out
=
dest
//
"tdg09.yaml"
in
let
tmp_ali_phy
=
dest
//
"tmp_ali.phy"
in
let
tmp_tree
=
dest
//
"tmp.nw"
in
let
package
=
tmp
//
"diffsel_script_utils.py"
in
let
script
=
tmp
//
"try_again.py"
in
workflow
~
descr
:
"convergence_detection.run_tdg09"
[
docker
env
(
and_list
[
mkdir_p
dest
;
mkdir_p
tmp
;
cd
tmp
;
cmd
"python"
[
file_dump
(
string
Scripts
.
rename_input_tree_ali_tdg09
)
;
opt
"-t"
dep
tree
;
...
...
@@ -22,11 +27,19 @@ let tdg09 ~(faa:aminoacid_fasta workflow) ~(tree:_ workflow) : [`tdg09] directo
opt
"-out_a "
ident
tmp_ali_phy
;
opt
"-out_t "
ident
tmp_tree
;
];
cmd
"tdg09.sh"
~
stdout
:
tdg09_out
[
cmd
"cp"
[
file_dump
(
string
Scripts
.
diffsel_script_utils
)
;
package
]
;
cmd
"cp"
[
file_dump
(
string
Scripts
.
try_again
)
;
script
]
;
cmd
"python"
~
stdout
:
tdg09_out
[
string
"try_again.py"
;
opt
"--timeout"
int
60
;
string
"
\"
tdg09.sh"
;
opt
"-tree"
ident
tmp_tree
;
opt
"-alignment"
ident
tmp_ali_phy
;
opt
"-threads"
int
1
;
opt
"-groups"
string
"XE ME"
;
string
"
\"
"
;
];
]
)
...
...
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