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genotoul-bioinfo
D-GENIES
Commits
91276b04
Commit
91276b04
authored
Apr 25, 2018
by
Floreal Cabanettes
Browse files
Fix find of errors in cluster mode + send mail on prepare fail
parent
97d7523e
Changes
2
Hide whitespace changes
Inline
Side-by-side
src/dgenies/bin/all_prepare.py
View file @
91276b04
...
...
@@ -46,7 +46,7 @@ def index_fasta(name, filepath, out_dir, type_f, dofilter = True):
os
.
remove
(
uncompressed
)
else
:
print
(
"###ERR## Error while indexing %s file: %s"
%
(
type_f
,
error
),
file
=
sys
.
stderr
)
print
(
"###ERR##
#
Error while indexing %s file: %s"
%
(
type_f
,
error
),
file
=
sys
.
stderr
)
if
uncompressed
is
not
None
:
try
:
os
.
remove
(
uncompressed
)
...
...
@@ -97,7 +97,7 @@ with open(args.preptime_file, "w") as ptime:
replace_fa
=
True
)
filter_f
.
filter
()
else
:
print
(
"###ERR## Error while loading query file: %s"
%
error
,
file
=
sys
.
stderr
)
print
(
"###ERR##
#
Error while loading query file: %s"
%
error
,
file
=
sys
.
stderr
)
exit
(
1
)
else
:
print
(
"Indexing query..."
)
...
...
src/dgenies/lib/job_manager.py
View file @
91276b04
...
...
@@ -819,12 +819,15 @@ class JobManager:
"-n"
,
self
.
query
.
get_name
()]
if
self
.
tool
.
split_before
:
args
.
append
(
"--split"
)
return
self
.
launch_to_cluster
(
step
=
"prepare"
,
batch_system_type
=
batch_system_type
,
command
=
self
.
config
.
cluster_python_exec
,
args
=
args
,
log_out
=
self
.
logs
,
log_err
=
self
.
logs
)
success
=
self
.
launch_to_cluster
(
step
=
"prepare"
,
batch_system_type
=
batch_system_type
,
command
=
self
.
config
.
cluster_python_exec
,
args
=
args
,
log_out
=
self
.
logs
,
log_err
=
self
.
logs
)
if
not
success
and
MODE
==
"webserver"
and
self
.
config
.
send_mail_status
:
self
.
send_mail_post
()
return
success
def
prepare_data_local
(
self
):
with
open
(
self
.
preptime_file
,
"w"
)
as
ptime
,
Job
.
connect
():
...
...
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