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VEBER Philippe
codepi
Commits
708615e3
Commit
708615e3
authored
Sep 04, 2018
by
Carine Rey
Browse files
put together all docker env versions
parent
98084400
Changes
17
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Showing
17 changed files
with
46 additions
and
34 deletions
+46
-34
lib/bppsuite.ml
lib/bppsuite.ml
+1
-1
lib/convergence_detection.ml
lib/convergence_detection.ml
+2
-2
lib/diffsel.ml
lib/diffsel.ml
+5
-5
lib/diffsel.mli
lib/diffsel.mli
+0
-1
lib/env.ml
lib/env.ml
+18
-0
lib/identical.ml
lib/identical.ml
+3
-3
lib/msd.ml
lib/msd.ml
+1
-1
lib/multinomial.ml
lib/multinomial.ml
+1
-1
lib/pcoc.ml
lib/pcoc.ml
+1
-1
lib/phyml.ml
lib/phyml.ml
+1
-1
lib/pipeline.ml
lib/pipeline.ml
+1
-1
lib/post_analyses.ml
lib/post_analyses.ml
+6
-9
lib/profile.ml
lib/profile.ml
+1
-2
lib/ready_dataset.ml
lib/ready_dataset.ml
+1
-2
lib/tamuri.ml
lib/tamuri.ml
+1
-1
lib/topological.ml
lib/topological.ml
+2
-2
lib/tree_dataset.ml
lib/tree_dataset.ml
+1
-1
No files found.
lib/bppsuite.ml
View file @
708615e3
...
...
@@ -6,7 +6,7 @@ open File_formats
type
bppseqgen_multi_profiles
let
env
=
docker_image
~
account
:
"carinerey"
~
name
:
"bppsuite"
~
tag
:
"07192018"
()
let
env
=
Env
.
env_bppsuite
let
assign
k
v
=
seq
~
sep
:
"="
[
string
k
;
v
]
...
...
lib/convergence_detection.ml
View file @
708615e3
...
...
@@ -42,7 +42,7 @@ type dataset_res = {
}
let
merge_results
?
fna_infos
~
res_by_tools
()
:
text_file
workflow
=
let
env
=
docker_image
~
account
:
"carinerey"
~
name
:
"python_basics"
~
tag
:
"07252018"
()
in
let
env
=
Env
.
env_py
in
let
fna_infos
=
match
fna_infos
with
|
Some
(
sw
)
->
sw
|
_
->
None
...
...
@@ -87,7 +87,7 @@ let merge_results ?fna_infos ~res_by_tools () : text_file workflow =
]
let
plot_merge_results
?
t_choices
~
plot_all_sites
~
(
res_by_tools
:
result
list
)
~
tree
~
faa
~
tsv
()
:
svg
workflow
=
let
env
=
docker_image
~
account
:
"carinerey"
~
name
:
"pcoc"
~
tag
:
"06212018"
()
in
let
env
=
Env
.
env_pcoc
in
(* use of pcoc env due to its working X server for dra plot with ete3 *)
let
meths
=
List
.
map
res_by_tools
~
f
:
(
fun
res
->
let
opt
=
match
res
with
...
...
lib/diffsel.ml
View file @
708615e3
...
...
@@ -62,8 +62,8 @@ echo end_it=$end_it
|
}
let
diffsel
~
(
phy_n
:
nucleotide_phylip
workflow
)
~
(
tree
:
_
workflow
)
~
(
w_every
:
int
)
~
(
n_cycles
:
int
)
~
(
id
:
int
)
~
tag
?
seed
()
:
[
`diffsel
]
directory
workflow
=
let
env
=
docker_image
~
account
:
"vlanore"
~
name
:
"diffsel"
~
tag
()
in
let
diffsel
~
(
phy_n
:
nucleotide_phylip
workflow
)
~
(
tree
:
_
workflow
)
~
(
w_every
:
int
)
~
(
n_cycles
:
int
)
~
(
id
:
int
)
?
seed
()
:
[
`diffsel
]
directory
workflow
=
let
env
=
Env
.
env_diffsel
in
let
tmp_tree
=
tmp
//
"myrun.tree"
in
let
tmp_ali
=
tmp
//
"myrun.ali"
in
let
dest_tree
=
dest
//
"myrun.tree"
in
...
...
@@ -73,7 +73,7 @@ let diffsel ~(phy_n:nucleotide_phylip workflow) ~(tree: _ workflow) ~(w_every:in
let
n_cycles
=
if
(
n_cycles
>
200
)
then
20
else
n_cycles
in
let
script_r
=
tmp
//
"DiffselMCMCConvergenceAnalysis.Rmd"
in
(*_build/diffsel -t data/samhd1.tree -d data/samhd1.ali -ncond 3 -x 1 10000 myrun*)
workflow
~
descr
:
(
"convergence_detection.run_diffsel."
^
tag
^
"."
^
(
string_of_int
id
))
[
workflow
~
descr
:
(
"convergence_detection.run_diffsel."
^
(
string_of_int
id
))
[
docker
env
(
and_list
[
mkdir_p
dest
;
...
...
@@ -98,7 +98,7 @@ 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
:
"07232018"
()
in
let
env
=
Env
.
env_r
in
let
script
=
tmp
//
"DiffselMCMCConvergenceAnalysis.Rmd"
in
let
trace
=
run_diffsel
/
selector
[
"myrun.trace"
]
in
let
out
=
dest
//
"out.html"
in
...
...
@@ -124,7 +124,7 @@ let check_conv run_diffsel : text_file directory workflow =
]
let
selector
run_diffsel
:
text_file
workflow
=
let
env
=
docker_image
~
account
:
"vlanore"
~
name
:
"diffsel"
~
tag
:
"master_a4b5"
()
in
let
env
=
Env
.
env_diffsel
in
let
package
=
tmp
//
"diffsel_script_utils.py"
in
let
script
=
tmp
//
"diffsel_analyze_result.py"
in
let
tmp_tree
=
tmp
//
"myrun.tree"
in
...
...
lib/diffsel.mli
View file @
708615e3
...
...
@@ -7,7 +7,6 @@ val diffsel :
w_every
:
int
->
n_cycles
:
int
->
id
:
int
->
tag
:
string
->
?
seed
:
int
->
unit
->
[
`diffsel
]
directory
workflow
...
...
lib/env.ml
0 → 100644
View file @
708615e3
open
Bistro
.
EDSL
let
env_bppsuite
=
docker_image
~
account
:
"carinerey"
~
name
:
"bppsuite"
~
tag
:
"09042018"
()
let
env_pcoc
=
docker_image
~
account
:
"carinerey"
~
name
:
"pcoc"
~
tag
:
"08312018"
()
let
env_tdg09
=
docker_image
~
account
:
"carinerey"
~
name
:
"tdg09_python"
~
tag
:
"v1.1.2fixed.31082018"
()
let
env_py
=
docker_image
~
account
:
"carinerey"
~
name
:
"python_basics"
~
tag
:
"07252018"
()
let
env_r
=
docker_image
~
account
:
"carinerey"
~
name
:
"r_basics"
~
tag
:
"08012018"
()
let
env_phyml
=
docker_image
~
account
:
"carinerey"
~
name
:
"phyml"
~
tag
:
"v3.1"
()
let
env_msd
=
docker_image
~
account
:
"carinerey"
~
name
:
"msd"
~
tag
:
"31082018"
()
let
env_diffsel
=
docker_image
~
account
:
"vlanore"
~
name
:
"diffsel"
~
tag
:
"master_a4b5"
()
lib/identical.ml
View file @
708615e3
...
...
@@ -34,7 +34,7 @@ let conf_file_bppml ~tree ~faa ~out ~config =
)
let
bppml
?
(
descr
=
""
)
~
faa
~
tree
~
config
:
_
workflow
=
let
env
=
docker_image
~
account
:
"carinerey"
~
name
:
"bppsuite"
~
tag
:
"07192018"
()
in
let
env
=
Env
.
env_bppsuite
in
let
config_f
=
dest
//
"config_bppml.bpp"
in
let
out
=
ident
dest
in
workflow
~
descr
:
(
"bppsuite.bppml"
^
descr
)
[
...
...
@@ -77,7 +77,7 @@ let conf_file_bppancestor ~tree ~faa ~out ~config =
)
let
bppancestor
?
(
descr
=
""
)
~
faa
~
tree
~
config
:
_
workflow
=
let
env
=
docker_image
~
account
:
"carinerey"
~
name
:
"bppsuite"
~
tag
:
"07192018"
()
in
let
env
=
Env
.
env_bppsuite
in
let
config_f
=
dest
//
"config_bppancestor.bpp"
in
let
out
=
ident
dest
in
workflow
~
descr
:
(
"bppsuite.bppancestor"
^
descr
)
[
...
...
@@ -98,7 +98,7 @@ let identical ~(tree_id:_ workflow) ~(tree_sc:_ workflow) ~(faa:aminoacid_fasta
let
out2
=
dest
//
"out2.tsv"
in
let
run_bppancestor
=
bppancestor
~
descr
:
""
~
tree
:
tree_id
~
faa
~
config
in
let
proba
=
run_bppancestor
/
selector
[
"sites.tsv"
]
in
let
env
=
docker_image
~
account
:
"carinerey"
~
name
:
"pcoc"
~
tag
:
"07022018"
()
in
let
env
=
Env
.
env_pcoc
in
workflow
~
descr
:
(
"identical."
^
prot_model
)
[
mkdir
dest
;
cmd
"python"
~
env
[
...
...
lib/msd.ml
View file @
708615e3
...
...
@@ -4,7 +4,7 @@ open Bistro.EDSL
open
Bistro_bioinfo
.
Std
open
File_formats
let
env
=
docker_image
~
account
:
"carinerey"
~
name
:
"msd"
~
tag
:
"31082018"
()
let
env
=
Env
.
env_msd
let
msd
~
e
~
(
faa
:
aminoacid_fasta
workflow
)
~
(
tree_sc
:_
workflow
)
:
[
`msd
]
directory
workflow
=
let
map_table
=
dest
//
"map.tsv"
in
...
...
lib/multinomial.ml
View file @
708615e3
...
...
@@ -5,7 +5,7 @@ open Bistro_bioinfo.Std
open
File_formats
let
multinomial
~
(
tree_id
:_
workflow
)
~
(
tree_sc
:_
workflow
)
~
(
faa
:
aminoacid_fasta
workflow
)
:
[
`multinomial
]
directory
workflow
=
let
env
=
docker_image
~
account
:
"carinerey"
~
name
:
"python_basics"
~
tag
:
"07252018"
()
in
let
env
=
Env
.
env_py
in
workflow
~
descr
:
(
"calc_multinomial"
)
[
mkdir_p
dest
;
cmd
"python"
~
env
[
...
...
lib/pcoc.ml
View file @
708615e3
...
...
@@ -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
:
"08312018"
()
in
let
env
=
Env
.
env_pcoc
in
workflow
~
descr
:
"convergence_detection.pcoc"
[
cmd
"pcoc_det.py"
~
env
[
opt
"-t"
dep
tree
;
...
...
lib/phyml.ml
View file @
708615e3
...
...
@@ -7,7 +7,7 @@ open File_formats
type
phyml
let
phyml
~
tree
phy
:
phyml
directory
workflow
=
let
env
=
docker_image
~
account
:
"carinerey"
~
name
:
"phyml"
~
tag
:
"v3.1"
()
in
let
env
=
Env
.
env_phyml
in
(*mpirun -np 4 phyml -o lr -u cyp_coding.ok.nwk -i cyp_coding.phy -d 'nt' -m gtr*)
let
tmp_phy
=
dest
//
"tree.phy"
in
workflow
~
descr
:
"phyml"
[
...
...
lib/pipeline.ml
View file @
708615e3
...
...
@@ -259,7 +259,7 @@ let derive_from_det_meth ~det_meth ~(dataset : Dataset.t) ~preview =
|
`Pcoc_gamma
->
`Pcoc_gamma
(
Pcoc
.
pcoc
~
catx_est
:
10
~
plot_complete
:
true
~
gamma
:
true
~
faa
~
tree
:
tree_sc
)
|
`Pcoc_C60
->
`Pcoc_C60
(
Pcoc
.
pcoc
~
catx_est
:
60
~
plot_complete
:
true
~
gamma
:
false
~
faa
~
tree
:
tree_sc
)
|
`Tdg09
->
`Tdg09
(
Tamuri
.
tdg09
~
faa
~
tree
:
tree_sc
)
|
`Diffsel
->
`Diffsel
(
Diffsel
.
diffsel
~
phy_n
~
tree
:
diffsel_tree
~
w_every
~
n_cycles
~
id
:
1
~
tag
:
"master_a4b5"
~
seed
()
)
|
`Diffsel
->
`Diffsel
(
Diffsel
.
diffsel
~
phy_n
~
tree
:
diffsel_tree
~
w_every
~
n_cycles
~
id
:
1
~
seed
()
)
|
`Identical_LG
->
`Identical_LG
(
Identical
.
identical
~
faa
~
tree_id
~
tree_sc
~
prot_model
:
"LG08"
)
|
`Identical_WAG
->
`Identical_WAG
(
Identical
.
identical
~
faa
~
tree_id
~
tree_sc
~
prot_model
:
"WAG01"
)
|
`Topological_LG
->
`Topological_LG
(
Topological
.
topological
~
faa
~
tree
:
tree_id
~
tree_conv
~
prot_model
:
"LG08"
)
...
...
lib/post_analyses.ml
View file @
708615e3
...
...
@@ -52,9 +52,6 @@ type post_analyses_simu = {
trees_plot
:
text_file
workflow
;
}
let
r_env
=
docker_image
~
account
:
"carinerey"
~
name
:
"r_basics"
~
tag
:
"08012018"
()
let
py_env
=
docker_image
~
account
:
"carinerey"
~
name
:
"python_basics"
~
tag
:
"07252018"
()
let
is_hyp
~
hyp
(
dataset_results
:
dataset_res
)
=
let
model_prefix
=
dataset_results
.
model_prefix
in
model_prefix
=
hyp
...
...
@@ -74,7 +71,7 @@ let make_t_choices ?(tree_prefix="") ~haPCOC_mr
~
h0_NeG5_indel_mr
~
haPC_NeG5_indel_mr
()
:
post_analyses_dir
directory
workflow
=
let
env
=
r_
env
in
let
env
=
Env
.
env
_r
in
let
out
=
dest
//
"out"
in
let
cmd_mr
=
List
.
map
[
(
"--H0_NeG1"
,
h0_NeG1_mr
);
...
...
@@ -111,7 +108,7 @@ 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
:
"08312018"
()
in
let
env
=
Env
.
env_pcoc
in
workflow
~
descr
:
(
"post_analyses.simu_infos."
^
descr
)
[
cmd
"python"
~
env
[
file_dump
(
string
Scripts
.
calc_simu_infos
)
;
...
...
@@ -123,7 +120,7 @@ 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
=
r_
env
in
let
env
=
Env
.
env
_r
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"
)]]
...
...
@@ -148,8 +145,8 @@ let group_simu_infos ~simu_infos_l : simu_infos directory workflow =
]
let
plot_trees
~
reinfered_tree_l
:
plot_trees
directory
workflow
=
let
env_r
=
r_
env
in
let
env_py
=
py_env
in
let
env_r
=
Env
.
env
_r
in
let
env_py
=
Env
.
env_py
in
let
cmd_cp_l
=
List
.
map
reinfered_tree_l
~
f
:
(
fun
rt
->
[
cmd
"cp"
[
dep
rt
.
reinfered_tree
;
tmp
//
(
rt
.
tree_prefix
^
"@"
^
rt
.
model_prefix
^
".nw"
)];
cmd
"cp"
[
dep
rt
.
input_tree
;
tmp
//
(
rt
.
tree_prefix
^
"@input_tree.nw"
)]
...
...
@@ -357,7 +354,7 @@ let post_analyses_simu_of_simu_dataset_l ~simu_dataset_l =
let
plot_sens_spe_t_choices
~
t_choices_l
~
dataset_results_l
~
profile_prefix
:
sens_spe_t_choices_plot
directory
workflow
=
let
env
=
r_
env
in
let
env
=
Env
.
env
_r
in
let
t_choices_dir
=
tmp
//
"t_choices_dir"
in
let
merged_results_dir
=
tmp
//
"merged_results_dir"
in
let
out
=
dest
//
"out"
in
...
...
lib/profile.ml
View file @
708615e3
...
...
@@ -9,9 +9,8 @@ type profile = {
profile_n
:
string
;
}
let
split_profile
~
nb_sites
~
dist_bins
profile_f
~
seed
:
text_file
directory
workflow
=
let
env
=
docker_image
~
account
:
"carinerey"
~
name
:
"python_basics"
~
tag
:
"07252018"
()
in
let
env
=
Env
.
env_py
in
let
package
=
tmp
//
"diffsel_script_utils.py"
in
let
script
=
tmp
//
"generate_pairs.py"
in
let
prefix
=
dest
//
"profile"
in
...
...
lib/ready_dataset.ml
View file @
708615e3
...
...
@@ -69,9 +69,8 @@ let paste d1 d2 =
let
ready_dataset
=
of_raw
{
Raw_dataset
.
input_tree
=
r_d1
.
input_tree
;
fna
;
fna_infos
}
in
ready_dataset
let
add_indels_to_fna
~
(
p
:
float
)
~
(
seed
:
int
)
(
fna
:
nucleotide_fasta
workflow
)
:
nucleotide_fasta
workflow
=
let
env
=
docker_image
~
account
:
"carinerey"
~
name
:
"python_basics"
~
tag
:
"07252018"
()
in
let
env
=
Env
.
env_py
in
workflow
~
descr
:
(
"add_indels"
)
[
cmd
"python"
~
env
[
file_dump
(
string
Scripts
.
add_indels
)
;
...
...
lib/tamuri.ml
View file @
708615e3
...
...
@@ -4,7 +4,7 @@ open Bistro.EDSL
open
Bistro_bioinfo
.
Std
open
File_formats
let
env
=
docker_image
~
account
:
"carinerey"
~
name
:
"tdg09_python"
~
tag
:
"v1.1.2fixed.31082018"
()
let
env
=
Env
.
env_tdg09
let
tdg09
~
(
faa
:
aminoacid_fasta
workflow
)
~
(
tree
:_
workflow
)
:
[
`tdg09
]
directory
workflow
=
let
tdg09_out
=
dest
//
"tdg09.yaml"
in
...
...
lib/topological.ml
View file @
708615e3
...
...
@@ -35,7 +35,7 @@ let conf_file_bppml ~tree ~faa ~out ~config =
)
let
bppml
?
(
descr
=
""
)
~
faa
~
tree
~
config
:
_
workflow
=
let
env
=
docker_image
~
account
:
"carinerey"
~
name
:
"bppsuite"
~
tag
:
"07192018"
()
in
let
env
=
Env
.
env_bppsuite
in
let
config_f
=
dest
//
"config_bppml.bpp"
in
let
out
=
ident
dest
in
workflow
~
descr
:
(
"bppsuite.bppml"
^
descr
)
[
...
...
@@ -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
:
"08312018"
()
in
let
env
=
Env
.
env_pcoc
in
workflow
~
descr
:
(
"topological.parse_"
^
prot_model
)
[
mkdir
dest
;
cmd
"cp"
[
dep
bppml_out
;
dest
//
"estimates.bppml_out.tsv"
];
...
...
lib/tree_dataset.ml
View file @
708615e3
...
...
@@ -3,7 +3,7 @@ open Bistro.EDSL
open
Bistro
.
Std
open
File_formats
let
env
=
docker_image
~
account
:
"carinerey"
~
name
:
"python_basics"
~
tag
:
"07252018"
()
let
env
=
Env
.
env_py
let
prepare
?
(
descr
=
""
)
tree
=
workflow
~
descr
:
(
"utils.parse_input_tree."
^
descr
)
[
...
...
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