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Docker-in-Docker (DinD) capabilities of public runners deactivated.
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VEBER Philippe
codepi
Commits
99b996a3
Commit
99b996a3
authored
Jul 10, 2018
by
Carine Rey
Browse files
add H0+Ha
parent
875124f2
Changes
4
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4 changed files
with
29 additions
and
3 deletions
+29
-3
lib/bppsuite.ml
lib/bppsuite.ml
+9
-0
lib/bppsuite.mli
lib/bppsuite.mli
+4
-0
lib/pipeline.ml
lib/pipeline.ml
+9
-3
lib/ready_dataset.ml
lib/ready_dataset.ml
+7
-0
No files found.
lib/bppsuite.ml
View file @
99b996a3
...
...
@@ -146,3 +146,12 @@ let fa2phy ~(fna: nucleotide_fasta workflow) : nucleotide_phylip workflow =
assign
"param"
(
file_dump
(
conf_file_bppseqman_fa2phy
~
fna
))
;
]
]
let
paste_fna
~
(
fna_l
:
nucleotide_fasta
workflow
list
)
:
nucleotide_fasta
workflow
=
workflow
~
descr
:
"bppsuite.catfasta"
[
cmd
"catfasta2phyml.pl"
~
stdout
:
dest
~
env
(
List
.
concat
[
[
string
"-f"
]
;
List
.
map
fna_l
~
f
:
(
fun
fna
->
dep
fna
)
;
])
]
lib/bppsuite.mli
View file @
99b996a3
...
...
@@ -25,3 +25,7 @@ val fna2faa :
val
fa2phy
:
fna
:
nucleotide_fasta
workflow
->
nucleotide_phylip
workflow
val
paste_fna
:
fna_l
:
nucleotide_fasta
workflow
list
->
nucleotide_fasta
workflow
lib/pipeline.ml
View file @
99b996a3
...
...
@@ -43,9 +43,15 @@ let derive_from_tree ~tree_dir ~tree ~profile_f ~preview =
H0NeBig
;
HaNeBig
;
]
in
List
.
map
models
~
f
:
(
fun
model
->
derive_from_model
~
model
~
tree
~
tree_dataset
~
tree_prefix
~
profile_f
~
preview
)
let
hypos
=
List
.
map
models
~
f
:
(
fun
model
->
derive_from_model
~
model
~
tree
~
tree_dataset
~
tree_prefix
~
profile_f
~
preview
)
in
let
ready_dataset_H0
=
(
derive_from_model
~
model
:
H0
~
tree
~
tree_dataset
~
tree_prefix
~
profile_f
~
preview
)
.
dataset
in
let
ready_dataset_Ha
=
(
derive_from_model
~
model
:
Ha
~
tree
~
tree_dataset
~
tree_prefix
~
profile_f
~
preview
)
.
dataset
in
let
hypos_concat
=
[{
Dataset
.
model_prefix
=
"H0+Ha"
;
tree_prefix
;
dataset
=
Ready_dataset
.
paste
ready_dataset_H0
ready_dataset_Ha
};]
in
List
.
concat
[
hypos
;
hypos_concat
]
let
derive_sim
~
tree_dir
~
trees
~
profile_fn
~
preview
=
let
profile_f
=
input
profile_fn
in
...
...
lib/ready_dataset.ml
View file @
99b996a3
...
...
@@ -33,3 +33,10 @@ let repo rd =
let
to_raw
{
input_tree
;
fna
}
=
{
Raw_dataset
.
input_tree
;
fna
}
let
paste
d1
d2
=
let
r_d1
=
to_raw
d1
in
let
r_d2
=
to_raw
d2
in
let
fna
=
Bppsuite
.
paste_fna
[
r_d1
.
fna
;
r_d2
.
fna
]
in
let
ready_dataset
=
of_raw
{
Raw_dataset
.
input_tree
=
r_d1
.
input_tree
;
fna
}
in
ready_dataset
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