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vidjil
vidjil
Commits
2958f7c0
Commit
2958f7c0
authored
Feb 23, 2016
by
HERBERT Ryan
Browse files
task.py added fuse
parent
e99363a7
Changes
1
Hide whitespace changes
Inline
Side-by-side
server/web2py/applications/vidjil/models/task.py
View file @
2958f7c0
...
@@ -200,7 +200,7 @@ def run_vidjil(id_file, id_config, id_data, id_fuse, grep_reads,
...
@@ -200,7 +200,7 @@ def run_vidjil(id_file, id_config, id_data, id_fuse, grep_reads,
return
"SUCCESS"
return
"SUCCESS"
def
run_mixcr
(
id_file
,
id_config
,
id_data
,
clean_before
=
False
,
clean_after
=
False
):
def
run_mixcr
(
id_file
,
id_config
,
id_data
,
id_fuse
,
clean_before
=
False
,
clean_after
=
False
):
from
subprocess
import
Popen
,
PIPE
,
STDOUT
,
os
from
subprocess
import
Popen
,
PIPE
,
STDOUT
,
os
import
time
import
time
...
@@ -266,6 +266,12 @@ def run_mixcr(id_file, id_config, id_data, clean_before=False, clean_after=False
...
@@ -266,6 +266,12 @@ def run_mixcr(id_file, id_config, id_data, clean_before=False, clean_after=False
res
=
{
"message"
:
"[%s] c%s: MiXCR finished - %s"
%
(
id_data
,
id_config
,
out_folder
)}
res
=
{
"message"
:
"[%s] c%s: MiXCR finished - %s"
%
(
id_data
,
id_config
,
out_folder
)}
log
.
info
(
res
)
log
.
info
(
res
)
for
row
in
db
(
db
.
sample_set_membership
.
sequence_file_id
==
id_file
).
select
()
:
sample_set_id
=
row
.
sample_set_id
print
row
.
sample_set_id
run_fuse
(
id_file
,
id_config
,
id_data
,
id_fuse
,
sample_set_id
,
clean_before
=
False
)
return
"SUCCESS"
return
"SUCCESS"
def
run_copy
(
id_file
,
id_config
,
id_data
,
id_fuse
,
clean_before
=
False
,
clean_after
=
False
):
def
run_copy
(
id_file
,
id_config
,
id_data
,
id_fuse
,
clean_before
=
False
,
clean_after
=
False
):
...
...
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