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genotoul-bioinfo
D-GENIES
Commits
6391ff30
Commit
6391ff30
authored
Nov 17, 2017
by
Floreal Cabanettes
Browse files
All-vs-All mode: select target, not query
parent
f68bd909
Changes
4
Hide whitespace changes
Inline
Side-by-side
bin/run_minimap2.sh
View file @
6391ff30
...
...
@@ -6,15 +6,12 @@ minimap_exec=$1
nb_threads
=
$2
fasta_t
=
$3
fasta_q
=
$4
query
=
$5
target
=
$6
paf
=
$7
paf_raw
=
$8
out_dir
=
$9
paf
=
$5
paf_raw
=
$6
# Run minimap:
if
[
"
$fasta_
t
"
!=
"NONE"
]
;
then
if
[
"
$fasta_
q
"
!=
"NONE"
]
;
then
echo
"Running:
${
minimap_exec
}
-t
${
nb_threads
}
${
fasta_t
}
${
fasta_q
}
>
${
paf_raw
}
"
...
...
@@ -22,9 +19,9 @@ ${minimap_exec} -t ${nb_threads} ${fasta_t} ${fasta_q} > ${paf_raw}
else
echo
"Running:
${
minimap_exec
}
-t
${
nb_threads
}
-X
${
fasta_
q
}
${
fasta_
q
}
>
${
paf_raw
}
"
echo
"Running:
${
minimap_exec
}
-t
${
nb_threads
}
-X
${
fasta_
t
}
${
fasta_
t
}
>
${
paf_raw
}
"
${
minimap_exec
}
-t
${
nb_threads
}
-X
${
fasta_
q
}
${
fasta_
q
}
>
${
paf_raw
}
${
minimap_exec
}
-t
${
nb_threads
}
-X
${
fasta_
t
}
${
fasta_
t
}
>
${
paf_raw
}
fi
...
...
js/dgenies.run.js
View file @
6391ff30
...
...
@@ -243,9 +243,9 @@ dgenies.run.valid_form = function () {
}
//Check input query:
if
(
$
(
"
input#
query
"
).
val
().
length
===
0
)
{
$
(
"
label.file-
query
"
).
addClass
(
"
error
"
);
dgenies
.
run
.
add_error
(
"
Query
fasta is required!
"
);
if
(
$
(
"
input#
target
"
).
val
().
length
===
0
)
{
$
(
"
label.file-
target
"
).
addClass
(
"
error
"
);
dgenies
.
run
.
add_error
(
"
Target
fasta is required!
"
);
has_errors
=
true
;
}
...
...
@@ -276,7 +276,7 @@ dgenies.run.reset_errors = function() {
dgenies
.
run
.
start_uploads
=
function
()
{
let
query_type
=
parseInt
(
$
(
"
select.query
"
).
val
());
if
(
query_type
===
0
)
{
if
(
query_type
===
0
&&
$
(
"
input#query
"
).
val
().
length
>
0
)
{
$
(
"
button#button-query
"
).
hide
();
dgenies
.
run
.
show_loading
(
"
query
"
);
}
...
...
lib/job_manager.py
View file @
6391ff30
...
...
@@ -84,10 +84,8 @@ class JobManager:
@
db_session
def
__launch_local
(
self
):
cmd
=
[
"run_minimap2.sh"
,
self
.
minimap2
,
self
.
threads
,
self
.
target
.
get_path
()
if
self
.
target
is
not
None
else
"NONE"
,
self
.
query
.
get_path
(),
self
.
query
.
get_name
(),
self
.
target
.
get_name
()
if
self
.
target
is
not
None
else
"NONE"
,
self
.
paf
,
self
.
paf_raw
,
self
.
output_dir
]
cmd
=
[
"run_minimap2.sh"
,
self
.
minimap2
,
self
.
threads
,
self
.
target
.
get_path
(),
self
.
query
.
get_path
()
if
self
.
query
is
not
None
else
"NONE"
,
self
.
paf
,
self
.
paf_raw
]
with
open
(
self
.
logs
,
"w"
)
as
logs
:
p
=
subprocess
.
Popen
(
cmd
,
stdout
=
logs
,
stderr
=
logs
)
job
=
Job
.
get
(
id_job
=
self
.
id_job
)
...
...
@@ -184,13 +182,13 @@ class JobManager:
job
=
Job
.
get
(
id_job
=
self
.
id_job
)
job
.
status
=
"indexing"
db
.
commit
()
query_index
=
os
.
path
.
join
(
self
.
output_dir
,
"query.idx"
)
Functions
.
index_file
(
self
.
query
,
query_index
)
target_index
=
os
.
path
.
join
(
self
.
output_dir
,
"target.idx"
)
if
self
.
target
is
not
None
:
Functions
.
index_file
(
self
.
target
,
target_index
)
Functions
.
index_file
(
self
.
target
,
target_index
)
query_index
=
os
.
path
.
join
(
self
.
output_dir
,
"query.idx"
)
if
self
.
query
is
not
None
:
Functions
.
index_file
(
self
.
query
,
query_index
)
else
:
shutil
.
copyfile
(
query
_index
,
target
_index
)
shutil
.
copyfile
(
target
_index
,
query
_index
)
job
=
Job
.
get
(
id_job
=
self
.
id_job
)
job
.
status
=
"success"
db
.
commit
()
...
...
@@ -210,7 +208,7 @@ class JobManager:
if
len
(
j1
)
>
0
:
print
(
"Old job found without result dir existing: delete it from BDD!"
)
j1
.
delete
()
if
self
.
query
is
not
None
:
if
self
.
target
is
not
None
:
job
=
Job
(
id_job
=
self
.
id_job
,
email
=
self
.
email
,
batch_type
=
self
.
batch_system_type
,
date_created
=
datetime
.
datetime
.
now
())
db
.
commit
()
...
...
srv/main.py
View file @
6391ff30
...
...
@@ -91,8 +91,8 @@ def launch_analysis():
if
email
==
""
:
errors
.
append
(
"Email not given"
)
form_pass
=
False
if
file_
query
==
""
:
errors
.
append
(
"No
query
fasta selected"
)
if
file_
target
==
""
:
errors
.
append
(
"No
target
fasta selected"
)
form_pass
=
False
# Form pass
...
...
@@ -107,16 +107,16 @@ def launch_analysis():
os
.
makedirs
(
folder_files
)
# Save files:
query
_name
=
os
.
path
.
splitext
(
file_query
.
replace
(
".gz"
,
""
))[
0
]
if
file_query_type
==
"local"
else
None
query_path
=
os
.
path
.
join
(
app
.
config
[
"UPLOAD_FOLDER"
],
session
[
"user_tmp_dir"
],
file_query
)
\
if
file_query_type
==
"local"
else
file_query
query
=
Fasta
(
name
=
query_name
,
path
=
query_path
,
type_f
=
file_query
_type
)
target
=
None
if
file_target
!=
""
:
target_name
=
os
.
path
.
splitext
(
file_target
.
replace
(
".gz"
,
""
))[
0
]
if
file_target_type
==
"local"
else
None
target_path
=
os
.
path
.
join
(
app
.
config
[
"UPLOAD_FOLDER"
],
session
[
"user_tmp_dir"
],
file_target
)
\
if
file_target_type
==
"local"
else
file_target
target
=
Fasta
(
name
=
target_name
,
path
=
target_path
,
type_f
=
file_target_type
)
query
=
None
if
file_query
!=
""
:
query_name
=
os
.
path
.
splitext
(
file_query
.
replace
(
".gz"
,
""
))[
0
]
if
file_query_type
==
"local"
else
None
query_path
=
os
.
path
.
join
(
app
.
config
[
"UPLOAD_FOLDER"
],
session
[
"user_tmp_dir"
],
file_query
)
\
if
file_query_type
==
"local"
else
file_query
query
=
Fasta
(
name
=
query_name
,
path
=
query_path
,
type_f
=
file_query_type
)
target_name
=
os
.
path
.
splitext
(
file_target
.
replace
(
".gz"
,
""
))[
0
]
if
file_target_type
==
"local"
else
None
target_path
=
os
.
path
.
join
(
app
.
config
[
"UPLOAD_FOLDER"
],
session
[
"user_tmp_dir"
],
file_target
)
\
if
file_target_type
==
"local"
else
file_target
target
=
Fasta
(
name
=
target_name
,
path
=
target_path
,
type_f
=
file_target_type
)
# Launch job:
job
=
JobManager
(
id_job
,
email
,
query
,
target
,
mailer
)
...
...
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