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VEBER Philippe
codepi
Commits
8a17aa45
Commit
8a17aa45
authored
Jul 23, 2018
by
Carine Rey
Browse files
update r_basics docker version (add pandoc)
parent
f10560c8
Changes
4
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4 changed files
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10 additions
and
5 deletions
+10
-5
etc/docker/r_basics/Dockerfile
etc/docker/r_basics/Dockerfile
+4
-0
etc/docker/r_basics/build_docker.sh
etc/docker/r_basics/build_docker.sh
+1
-1
lib/diffsel.ml
lib/diffsel.ml
+1
-1
lib/post_analyses.ml
lib/post_analyses.ml
+4
-3
No files found.
etc/docker/r_basics/Dockerfile
View file @
8a17aa45
...
...
@@ -4,3 +4,7 @@ MAINTAINER Carine Rey carine.rey@ens-lyon.org
RUN
echo
'install.packages(c("optparse", "ggplot2", "reshape2", "cowplot", "coda"), repos="https://mirror.ibcp.fr/pub/CRAN/", dependencies=TRUE)'
>
/tmp/packages.R
\
&&
Rscript /tmp/packages.R
RUN
apt-get update
&&
\
apt-get
install
--no-install-recommends
-qy
\
pandoc
etc/docker/r_basics/build_docker.sh
View file @
8a17aa45
...
...
@@ -4,7 +4,7 @@ set -e
IMAGE_NAME
=
r_basics
DOCKERFILE_DIR
=
.
TAG
=
07
16
2018
TAG
=
07
23
2018
REPO
=
carinerey/
$IMAGE_NAME
:
$TAG
docker build
-t
$REPO
-f
./Dockerfile
$DOCKERFILE_DIR
...
...
lib/diffsel.ml
View file @
8a17aa45
...
...
@@ -32,7 +32,7 @@ let diffsel ~(phy_n:nucleotide_phylip workflow) ~(tree: _ workflow) ~(w_every:in
]
let
check_conv
run_diffsel
:
text_file
directory
workflow
=
let
env
=
docker_image
~
account
:
"carinerey"
~
name
:
"r_basics"
~
tag
:
"07
16
2018"
()
in
let
env
=
docker_image
~
account
:
"carinerey"
~
name
:
"r_basics"
~
tag
:
"07
23
2018"
()
in
let
script
=
tmp
//
"DiffselMCMCConvergenceAnalysis.Rmd"
in
let
trace
=
run_diffsel
/
selector
[
"myrun.trace"
]
in
let
out
=
dest
//
"out.html"
in
...
...
lib/post_analyses.ml
View file @
8a17aa45
...
...
@@ -40,13 +40,14 @@ type post_analyses_simu = {
simu_infos_plot
:
text_file
workflow
;
}
let
r_env
=
docker_image
~
account
:
"carinerey"
~
name
:
"r_basics"
~
tag
:
"07232018"
()
let
is_hyp
~
hyp
(
dataset_results
:
dataset_res
)
=
let
model_prefix
=
dataset_results
.
model_prefix
in
model_prefix
=
hyp
let
make_t_choices
~
h0_merged_results
~
ha_merged_results
:
post_analyses_dir
directory
workflow
=
let
env
=
docker_image
~
account
:
"carinerey"
~
name
:
"r_basics"
~
tag
:
"07162018"
()
in
let
env
=
r_env
in
let
out
=
dest
//
"out"
in
workflow
~
descr
:
"post_analyses.t_choices"
[
docker
env
(
...
...
@@ -74,7 +75,7 @@ let make_simu_infos ?(descr="") ?(fna_infos) ~faa ~tree_sc : text_file workflow
]
let
group_simu_infos
~
simu_infos_l
:
simu_infos
directory
workflow
=
let
env
=
docker_image
~
account
:
"carinerey"
~
name
:
"r_basics"
~
tag
:
"07162018"
()
in
let
env
=
r_env
in
let
cmd_cp_l
=
List
.
map
simu_infos_l
~
f
:
(
fun
s
->
match
s
.
simu_infos
with
|
Some
w
->
[
cmd
"cp"
[
dep
w
;
tmp
//
(
s
.
tree_prefix
^
"@"
^
s
.
model_prefix
^
".tsv"
)]]
...
...
@@ -163,7 +164,7 @@ let post_analyses_simu_of_simu_dataset_l ~simu_dataset_l =
let
plot_sens_spe_t_choices
~
t_choices_l
~
dataset_results_l
~
profile
:
sens_spe_t_choices_plot
directory
workflow
=
let
env
=
docker_image
~
account
:
"carinerey"
~
name
:
"r_basics"
~
tag
:
"07162018"
()
in
let
env
=
r_env
in
let
t_choices_dir
=
tmp
//
"t_choices_dir"
in
let
merged_results_dir
=
tmp
//
"merged_results_dir"
in
let
out
=
dest
//
"out"
in
...
...
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