Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Sign in
Toggle navigation
Open sidebar
ensembl-gh-mirror
ensembl-hive
Commits
8f430089
Commit
8f430089
authored
May 17, 2012
by
Leo Gordon
Browse files
rename meadow_name to meadow_type to match the rest of the repository, before it is too late
parent
16997244
Changes
1
Hide whitespace changes
Inline
Side-by-side
Showing
1 changed file
with
7 additions
and
7 deletions
+7
-7
scripts/beekeeper.pl
scripts/beekeeper.pl
+7
-7
No files found.
scripts/beekeeper.pl
View file @
8f430089
...
...
@@ -40,7 +40,7 @@ sub main {
my
$no_pend_adjust
=
0
;
my
$submit_workers_max
=
50
;
my
$total_workers_max
=
undef
;
my
$meadow_
nam
e
=
undef
;
my
$meadow_
typ
e
=
undef
;
my
$meadow_options
=
'';
my
$run
=
0
;
my
$max_loops
=
0
;
# not running by default
...
...
@@ -87,7 +87,7 @@ sub main {
'
total_workers_max|local_cpus=i
'
=>
\
$total_workers_max
,
'
submit_workers_max|wlimit=i
'
=>
\
$submit_workers_max
,
'
no_pend
'
=>
\
$no_pend_adjust
,
'
meadow_
nam
e=s
'
=>
\
$meadow_
nam
e
,
'
meadow_
typ
e=s
'
=>
\
$meadow_
typ
e
,
'
meadow_options=s
'
=>
\
$meadow_options
,
# worker control
...
...
@@ -170,8 +170,8 @@ sub main {
print
STDERR
"
+---------------------------------------------------------------------+
\n
";
}
$meadow_
nam
e
=
'
LOCAL
'
if
(
$local
);
my
$valley
=
Bio::EnsEMBL::Hive::
Valley
->
new
(
-
current_meadow_class
=>
$meadow_
nam
e
);
$meadow_
typ
e
=
'
LOCAL
'
if
(
$local
);
my
$valley
=
Bio::EnsEMBL::Hive::
Valley
->
new
(
-
current_meadow_class
=>
$meadow_
typ
e
);
my
$current_meadow_class
=
$valley
->
current_meadow_class
();
warn
"
Current meadow: '
$current_meadow_class
'
\n
";
...
...
@@ -442,8 +442,8 @@ __DATA__
# Do not run any additional Workers, just check for the current status of the pipeline:
beekeeper.pl -url mysql://username:secret@hostname:port/ehive_dbname
# Run the pipeline in automatic mode (-loop), run all the workers locally (-meadow_
nam
e LOCAL) and allow for 3 parallel workers (-total_workers_max 3)
beekeeper.pl -url mysql://username:secret@hostname:port/long_mult_test -meadow_
nam
e LOCAL -total_workers_max 3 -loop
# Run the pipeline in automatic mode (-loop), run all the workers locally (-meadow_
typ
e LOCAL) and allow for 3 parallel workers (-total_workers_max 3)
beekeeper.pl -url mysql://username:secret@hostname:port/long_mult_test -meadow_
typ
e LOCAL -total_workers_max 3 -loop
# Run in automatic mode, but only restrict to running the 'fast_blast' analysis
beekeeper.pl -url mysql://username:secret@hostname:port/long_mult_test -logic_name fast_blast -loop
...
...
@@ -485,7 +485,7 @@ __DATA__
-total_workers_max <num> : max # workers to be running in parallel
-submit_workers_max <num> : max # workers to create per loop
-no_pend : don't adjust needed workers by pending workers
-meadow_
nam
e <string> : the desired Meadow class name, such as 'LSF' or 'LOCAL'
-meadow_
typ
e <string> : the desired Meadow class name, such as 'LSF' or 'LOCAL'
-meadow_options <string> : passes <string> to the Meadow submission command as <options> (formerly lsf_options)
=head2 Worker control
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment