# 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>
<pre>
beekeeper.pl -url mysql://username:secret@hostname:port/long_mult_test -meadow_type LOCAL -total_running_workers_max 3 -loop
# 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'
-total_running_workers_max <num> : max # workers to be running in parallel
-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)
-submit_log_dir <dir> : record submission output+error streams into files under the given directory (to see why some workers fail after submission)</pre>
-analyses_pattern <string> : restrict the sync operation, printing of stats or looping of the beekeeper to the specified subset of analyses
-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>
<h2id="Worker-control">Worker control</h2>
<pre><code> -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
-life_span <num> : life_span limit for each worker
-life_span <num> : number of minutes each worker is allowed to run
-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?
-hive_log_dir <path> : directory where stdout/stderr of the hive is redirected
-debug <debug_level> : set debug level of the workers</pre>
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.
See the License for the specific language governing permissions and limitations under the License.</pre>
<p>
</p>
<hr/>
<h1><aname="contact">CONTACT</a></h1>
<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>
See the License for the specific language governing permissions and limitations under the License.</code></pre>
<h1id="CONTACT">CONTACT</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><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.
-url is exclusive to -reg_alias. -reg_type is only needed if several databases map to that alias / species.</code></pre>
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.
See the License for the specific language governing permissions and limitations under the License.</pre>
<p>
</p>
<hr/>
<h1><aname="contact">CONTACT</a></h1>
<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>
See the License for the specific language governing permissions and limitations under the License.</code></pre>
<h1id="CONTACT">CONTACT</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>
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.
See the License for the specific language governing permissions and limitations under the License.</pre>
<p>
</p>
<hr/>
<h1><aname="contact">CONTACT</a></h1>
<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>
See the License for the specific language governing permissions and limitations under the License.</code></pre>
<h1id="CONTACT">CONTACT</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>
<p>This script is used for offline examination of the allocation of workers.</p>
<p>Based on the command-line parameters 'start_date' and 'end_date', or on the start time of the first
worker and end time of the last worker (as recorded in pipeline DB), it pulls the relevant data out
of the 'worker' table for accurate timing.
By default, the output is in CSV format, to allow extra analysis to be carried.</p>
<p>Based on the command-line parameters 'start_date' and 'end_date', or on the start time of the first worker and end time of the last worker (as recorded in pipeline DB), it pulls the relevant data out of the 'worker' table for accurate timing. By default, the output is in CSV format, to allow extra analysis to be carried.</p>
<p>You can optionally ask the script to generate an image with Gnuplot.</p>
