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VEBER Philippe
codepi
Commits
9443ef17
Commit
9443ef17
authored
Aug 31, 2018
by
LANORE Vincent
Browse files
Updated tdg09 docker with fixed tdg09
parent
9e81940a
Changes
4
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4 changed files
with
7 additions
and
15 deletions
+7
-15
etc/docker/tamuri/Dockerfile
etc/docker/tamuri/Dockerfile
+2
-7
etc/docker/tamuri/build_docker.sh
etc/docker/tamuri/build_docker.sh
+1
-1
etc/docker/tamuri/tdg09.jar
etc/docker/tamuri/tdg09.jar
+0
-0
lib/tamuri.ml
lib/tamuri.ml
+4
-7
No files found.
etc/docker/tamuri/Dockerfile
View file @
9443ef17
...
...
@@ -26,9 +26,4 @@ RUN pip install docopt==0.6.2
# getting tdg09
WORKDIR
/tdg09
RUN
wget https://github.com/tamuri/tdg09/archive/v1.1.2.tar.gz
&&
\
tar
xzf v1.1.2.tar.gz
&&
\
rm
v1.1.2.tar.gz
&&
\
printf
"#!/bin/bash
\
\n
java -cp /tdg09/tdg09-1.1.2/dist/tdg09.jar tdg09.Analyse
\$
@
\
\n
"
>
/usr/bin/tdg09.sh
&&
chmod
+x /usr/bin/tdg09.sh
COPY
tdg09.jar .
etc/docker/tamuri/build_docker.sh
View file @
9443ef17
...
...
@@ -4,7 +4,7 @@ set -e
IMAGE_NAME
=
tdg09_python
DOCKERFILE_DIR
=
.
TAG
=
v1.1.2
_07
102018
TAG
=
v1.1.2
fixed.3
10
8
2018
REPO
=
carinerey/
$IMAGE_NAME
:
$TAG
docker build
-t
$REPO
-f
./Dockerfile
$DOCKERFILE_DIR
...
...
etc/docker/tamuri/tdg09.jar
0 → 100644
View file @
9443ef17
File added
lib/tamuri.ml
View file @
9443ef17
...
...
@@ -4,7 +4,7 @@ open Bistro.EDSL
open
Bistro_bioinfo
.
Std
open
File_formats
let
env
=
docker_image
~
account
:
"carinerey"
~
name
:
"tdg09_python"
~
tag
:
"v1.1.2
_07
102018"
()
let
env
=
docker_image
~
account
:
"carinerey"
~
name
:
"tdg09_python"
~
tag
:
"v1.1.2
fixed.3
10
8
2018"
()
let
tdg09
~
(
faa
:
aminoacid_fasta
workflow
)
~
(
tree
:_
workflow
)
:
[
`tdg09
]
directory
workflow
=
let
tdg09_out
=
dest
//
"tdg09.yaml"
in
...
...
@@ -30,16 +30,13 @@ let tdg09 ~(faa:aminoacid_fasta workflow) ~(tree:_ workflow) : [`tdg09] directo
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
240
;
string
"
\"
java -cp /tdg09/tdg09-1.1.2/dist/tdg09.jar tdg09.Analyse"
;
cmd
"java"
~
stdout
:
tdg09_out
[
string
"-cp /tdg09/tdg09.jar tdg09.Analyse"
;
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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