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ensembl-gh-mirror
ensembl-hive
Commits
b2bcfd6f
Commit
b2bcfd6f
authored
Jul 09, 2004
by
Jessica Severin
Browse files
a bit of cleanup
parent
b2513329
Changes
1
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1 changed file
with
8 additions
and
15 deletions
+8
-15
scripts/lsf_beekeeper.pl
scripts/lsf_beekeeper.pl
+8
-15
No files found.
scripts/lsf_beekeeper.pl
View file @
b2bcfd6f
...
...
@@ -20,9 +20,6 @@ $self->{'db_conf'} = {};
$self
->
{'
db_conf
'}
->
{'
-user
'}
=
'
ensro
';
$self
->
{'
db_conf
'}
->
{'
-port
'}
=
3306
;
$self
->
{'
analysis_id
'}
=
undef
;
$self
->
{'
outdir
'}
=
"
/ecs4/work2/ensembl/jessica/data/hive-output
";
my
$conf_file
;
my
(
$help
,
$host
,
$user
,
$pass
,
$dbname
,
$port
,
$adaptor
,
$url
);
my
(
$limit
,
$batch_size
);
...
...
@@ -35,14 +32,12 @@ GetOptions('help' => \$help,
'
dbuser=s
'
=>
\
$user
,
'
dbpass=s
'
=>
\
$pass
,
'
dbname=s
'
=>
\
$dbname
,
'
dead
'
=>
\
$self
->
{'
all
_dead
'},
'
run
'
=>
\
$self
->
{'
run
'},
'
dead
'
=>
\
$self
->
{'
check_for
_dead
'},
'
run
'
=>
\
$self
->
{'
run
'},
'
limit=i
'
=>
\
$limit
,
'
batch_size=i
'
=>
\
$batch_size
);
$self
->
{'
analysis_id
'}
=
shift
if
(
@
_
);
if
(
$help
)
{
usage
();
}
parse_conf
(
$self
,
$conf_file
);
...
...
@@ -74,7 +69,9 @@ if($url) {
my
$queen
=
$DBA
->
get_Queen
;
if
(
$self
->
{'
all_dead
'})
{
check_for_dead_workers
(
$self
,
$queen
);
}
if
(
$self
->
{'
check_for_dead
'})
{
check_for_dead_workers
(
$self
,
$queen
);
}
$queen
->
get_hive_current_load
();
$queen
->
update_analysis_stats
();
$queen
->
check_blocking_control_rules
;
...
...
@@ -95,7 +92,7 @@ exit(0);
#######################
sub
usage
{
print
"
l
ocal
_beekeeper.pl [options]
\n
";
print
"
l
sf
_beekeeper.pl [options]
\n
";
print
"
-help : print this help
\n
";
print
"
-url <url string> : url defining where hive database is located
\n
";
print
"
-conf <path> : config file describing db connection
\n
";
...
...
@@ -108,7 +105,7 @@ sub usage {
print
"
-limit <num> : #jobs to run before worker can die naturally
\n
";
print
"
-run : show and run the needed jobs
\n
";
print
"
-dead : clean overdue jobs for resubmission
\n
";
print
"
l
ocal
_beekeeper.pl v1.0
\n
";
print
"
l
sf
_beekeeper.pl v1.0
\n
";
exit
(
1
);
}
...
...
@@ -165,10 +162,6 @@ sub run_next_worker_clutch
else
{
$cmd
=
"
bsub -JW
$analysis_id
$worker_cmd
";}
print
("
$cmd
\n
");
system
(
$cmd
)
if
(
$self
->
{'
run
'});
# return of bsub looks like this
#Job <6392054> is submitted to default queue <normal>.
}
}
...
...
@@ -191,7 +184,7 @@ sub check_for_dead_workers {
$queen
->
register_worker_death
(
$worker
);
}
else
{
print
("
ALIVE and running
\n
");
print
("
ALIVE and running
\n
");
}
}
}
...
...
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