# Run the pipeline in automatic mode (-loop), run all the workers locally (-meadow_type LOCAL) and allow for 3 parallel workers (-total_running_workers_max 3)
# Run the pipeline in automatic mode (-loop), run all the workers locally (-meadow_type LOCAL) and allow for 3 parallel workers (-total_running_workers_max 3)
beekeeper.pl -url mysql://username:secret@hostname:port/long_mult_test -meadow_type LOCAL -total_running_workers_max 3 -loop</pre>
beekeeper.pl -url mysql://username:secret@hostname:port/long_mult_test -meadow_type LOCAL -total_running_workers_max 3 -loop
<pre>
# Run in automatic mode, but only restrict to running blast-related analyses with the exception of analyses 4..6
# Run in automatic mode, but only restrict to running blast-related analyses with the exception of analyses 4..6
<pre><code> -meadow_type <string> : the desired Meadow class name, such as 'LSF' or 'LOCAL'
-meadow_type <string> : the desired Meadow class name, such as 'LSF' or 'LOCAL'
-total_running_workers_max <num> : max # workers to be running in parallel
-total_running_workers_max <num> : max # workers to be running in parallel
-submit_workers_max <num> : max # workers to create per loop iteration
-submit_workers_max <num> : max # workers to create per loop iteration
-submission_options <string> : passes <string> to the Meadow submission command as <options> (formerly lsf_options)
-submission_options <string> : passes <string> to the Meadow submission command as <options> (formerly lsf_options)
-submit_log_dir <dir> : record submission output+error streams into files under the given directory (to see why some workers fail after submission)</pre>
-submit_log_dir <dir> : record submission output+error streams into files under the given directory (to see why some workers fail after submission)</code></pre>
<pre><code> -analyses_pattern <string> : restrict the sync operation, printing of stats or looping of the beekeeper to the specified subset of analyses
-analyses_pattern <string> : restrict the sync operation, printing of stats or looping of the beekeeper to the specified subset of analyses
-can_respecialize <0|1> : allow workers to re-specialize into another analysis (within resource_class) after their previous analysis was exhausted
-can_respecialize <0|1> : allow workers to re-specialize into another analysis (within resource_class) after their previous analysis was exhausted
-force : run all workers with -force (see runWorker.pl)
-force : run all workers with -force (see runWorker.pl)
-killworker <worker_id> : kill worker by worker_id
-killworker <worker_id> : kill worker by worker_id
...
@@ -132,12 +88,11 @@
...
@@ -132,12 +88,11 @@
-job_limit <num> : #jobs to run before worker can die naturally
-job_limit <num> : #jobs to run before worker can die naturally
-retry_throwing_jobs <0|1> : if a job dies *knowingly*, should we retry it by default?
-retry_throwing_jobs <0|1> : if a job dies *knowingly*, should we retry it by default?
-hive_log_dir <path> : directory where stdout/stderr of the hive is redirected
-hive_log_dir <path> : directory where stdout/stderr of the hive is redirected
-debug <debug_level> : set debug level of the workers</pre>
-debug <debug_level> : set debug level of the workers</code></pre>
Unless required by applicable law or agreed to in writing, software distributed under the License
Unless required by applicable law or agreed to in writing, software distributed under the License
is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and limitations under the License.</pre>
See the License for the specific language governing permissions and limitations under the License.</code></pre>
<p>
</p>
<h1id="CONTACT">CONTACT</h1>
<hr/>
<h1><aname="contact">CONTACT</a></h1>
<pre><code> Please subscribe to the Hive mailing list: http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users to discuss Hive-related questions or to be notified of our updates</code></pre>
<pre>
Please subscribe to the Hive mailing list: <ahref="http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users">http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users</a> to discuss Hive-related questions or to be notified of our updates</pre>
<pre><code> db_cmd.pl is a generic script that connects you interactively to your database using either URL or Registry and optionally runs an SQL command.
db_cmd.pl is a generic script that connects you interactively to your database using either URL or Registry and optionally runs an SQL command.
-url is exclusive to -reg_alias. -reg_type is only needed if several databases map to that alias / species.
-url is exclusive to -reg_alias. -reg_type is only needed if several databases map to that alias / species.
If the arguments that have to be appended contain options (i.e. start with dashes), first use a double-dash to indicate the end of db_cmd.pl's options and the start of the arguments that have to be passed as-is (see the example below with --html)</pre>
If the arguments that have to be appended contain options (i.e. start with dashes), first use a double-dash to indicate the end of db_cmd.pl's options and the start of the arguments that have to be passed as-is (see the example below with --html)</code></pre>
Unless required by applicable law or agreed to in writing, software distributed under the License
Unless required by applicable law or agreed to in writing, software distributed under the License
is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and limitations under the License.</pre>
See the License for the specific language governing permissions and limitations under the License.</code></pre>
<p>
</p>
<h1id="CONTACT">CONTACT</h1>
<hr/>
<h1><aname="contact">CONTACT</a></h1>
<pre><code> Please subscribe to the Hive mailing list: http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users to discuss Hive-related questions or to be notified of our updates</code></pre>
<pre>
Please subscribe to the Hive mailing list: <ahref="http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users">http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users</a> to discuss Hive-related questions or to be notified of our updates</pre>
Unless required by applicable law or agreed to in writing, software distributed under the License
Unless required by applicable law or agreed to in writing, software distributed under the License
is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and limitations under the License.</pre>
See the License for the specific language governing permissions and limitations under the License.</code></pre>
<p>
</p>
<h1id="CONTACT">CONTACT</h1>
<hr/>
<h1><aname="contact">CONTACT</a></h1>
<pre><code> Please subscribe to the Hive mailing list: http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users to discuss Hive-related questions or to be notified of our updates</code></pre>
<pre>
Please subscribe to the Hive mailing list: <ahref="http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users">http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users</a> to discuss Hive-related questions or to be notified of our updates</pre>
