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VEBER Philippe
codepi
Commits
6fab92e8
Commit
6fab92e8
authored
Aug 31, 2018
by
Carine Rey
Browse files
update pcoc version (take into account indels)
parent
aa74e39b
Changes
5
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5 changed files
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and
5 deletions
+5
-5
etc/docker/pcoc/Dockerfile
etc/docker/pcoc/Dockerfile
+1
-1
etc/docker/pcoc/build_docker.sh
etc/docker/pcoc/build_docker.sh
+1
-1
lib/pcoc.ml
lib/pcoc.ml
+1
-1
lib/post_analyses.ml
lib/post_analyses.ml
+1
-1
lib/topological.ml
lib/topological.ml
+1
-1
No files found.
etc/docker/pcoc/Dockerfile
View file @
6fab92e8
...
...
@@ -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
View file @
6fab92e8
...
...
@@ -4,7 +4,7 @@ set -e
IMAGE_NAME
=
pcoc
DOCKERFILE_DIR
=
.
TAG
=
0
702
2018
TAG
=
0
831
2018
REPO
=
carinerey/
$IMAGE_NAME
:
$TAG
docker build
-t
$REPO
-f
./Dockerfile
$DOCKERFILE_DIR
...
...
lib/pcoc.ml
View file @
6fab92e8
...
...
@@ -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
:
"0
702
2018"
()
in
let
env
=
docker_image
~
account
:
"carinerey"
~
name
:
"pcoc"
~
tag
:
"0
831
2018"
()
in
workflow
~
descr
:
"convergence_detection.pcoc"
[
cmd
"pcoc_det.py"
~
env
[
opt
"-t"
dep
tree
;
...
...
lib/post_analyses.ml
View file @
6fab92e8
...
...
@@ -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
:
"0
702
2018"
()
in
let
env
=
docker_image
~
account
:
"carinerey"
~
name
:
"pcoc"
~
tag
:
"0
831
2018"
()
in
workflow
~
descr
:
(
"post_analyses.simu_infos."
^
descr
)
[
cmd
"python"
~
env
[
file_dump
(
string
Scripts
.
calc_simu_infos
)
;
...
...
lib/topological.ml
View file @
6fab92e8
...
...
@@ -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
:
"0
702
2018"
()
in
let
env
=
docker_image
~
account
:
"carinerey"
~
name
:
"pcoc"
~
tag
:
"0
831
2018"
()
in
workflow
~
descr
:
(
"topological.parse_"
^
prot_model
)
[
mkdir
dest
;
cmd
"cp"
[
dep
bppml_out
;
dest
//
"estimates.bppml_out.tsv"
];
...
...
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