Added scripts documentation

3172e1fd · Matthieu Muffato · 24a3a417 · 3172e1fd · 3172e1fd · 3172e1fd
Commit 3172e1fd authored 10 years ago by Matthieu Muffato
--- a/docs/ehive_doc.css
+++ b/docs/ehive_doc.css
@@ -30,6 +30,9 @@ pre, code, kbd { font-family: Courier New, Courier, monospace; }
 div, span, p, li, dd, dt, pre, code, kbd { font-size: 1em; }
 th, td { font-size: 0.8em; }

+div.tree { line-height: 1.1em }
+div.tree span.tree {font-family: Times New Roman; Courier New, Courier, monospace; }
+
 body.ie6 th, body.ie6 td { font-size: 13px; }

 /*----------------------------------------------------------------------

--- a/docs/index.html
+++ b/docs/index.html
@@ -17,6 +17,21 @@ The name &quot;Hive&quot; comes from the way pipelines are processed by a swarm
 	<li>Introduction to eHive: <a href="presentations/HiveWorkshop_Sept2013/">Sept. 2013 workshop</a> (parts <a href="presentations/HiveWorkshop_Sept2013/Slides_part1.pdf">1</a>, <a href="presentations/HiveWorkshop_Sept2013/Slides_part2.pdf">2</a> and <a href="presentations/HiveWorkshop_Sept2013/Slides_part3.pdf">3</a> in PDF)</li>
 	<li><a href="install.html">Dependencies, installation and setup</a></li>
 	<li><a href="hive_schema.html">Database schema</a></li>
+	<li class="tree">eHive scripts<br>
+	<div class="tree">
+	<span class="tree">│   </span><em>Execution</em><br>
+	<span class="tree">├── </span><a href="scripts/init_pipeline.html">init_pipeline</a><br>
+	<span class="tree">├── </span><a href="scripts/seed_pipeline.html">seed_pipeline</a><br>
+	<span class="tree">├── </span><a href="scripts/beekeeper.html">beekeeper</a><br>
+	<span class="tree">│   </span><em>Debugging</em><br>
+	<span class="tree">├── </span><a href="scripts/runWorker.html">runWorker</a><br>
+	<span class="tree">├── </span><a href="scripts/db_cmd.html">db_cmd</a><br>
+	<span class="tree">├── </span><a href="scripts/standaloneJob.html">standaloneJob</a><br>
+	<span class="tree">├── </span><a href="scripts/hoover_pipeline.html">hoover_pipeline</a><br>
+	<span class="tree">│   </span><em>Reporting</em><br>
+	<span class="tree">├── </span><a href="scripts/generate_graph.html">generate_graph</a><br>
+	<span class="tree">├── </span><a href="scripts/lsf_report.html">lsf_report</a><br>
+	<span class="tree">└── </span><a href="scripts/generate_timeline.html">generate_timeline</a><br>
 </div>
 </li>


--- a/docs/scripts/beekeeper.html
+++ b/docs/scripts/beekeeper.html
+<?xml version="1.0" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title>beekeeper.pl</title>
+<meta http-equiv="content-type" content="text/html; charset=utf-8" />
+<link rev="made" href="mailto:root@localhost" />
+</head>
+
+<body style="background-color: white">
+
+
+
+<h1 id="NAME">NAME</h1>
+
+<pre><code>    beekeeper.pl</code></pre>
+
+<h1 id="DESCRIPTION">DESCRIPTION</h1>
+
+<pre><code>    The Beekeeper is in charge of interfacing between the Queen and a compute resource or &#39;compute farm&#39;.
+    Its job is to initialize/sync the eHive database (via the Queen), query the Queen if it needs any workers
+    and to send the requested number of workers to open machines via the runWorker.pl script.
+
+    It is also responsible for interfacing with the Queen to identify workers which died
+    unexpectedly so that she can free the dead workers and reclaim unfinished jobs.</code></pre>
+
+<h1 id="USAGE-EXAMPLES">USAGE EXAMPLES</h1>
+
+<pre><code>        # Usually run after the pipeline has been created to calculate the internal statistics necessary for eHive functioning
+    beekeeper.pl -url mysql://username:secret@hostname:port/ehive_dbname -sync
+
+        # 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_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
+
+        # Run in automatic mode, but only restrict to running the &#39;fast_blast&#39; analysis
+    beekeeper.pl -url mysql://username:secret@hostname:port/long_mult_test -logic_name fast_blast -loop
+
+        # Restrict the normal execution to one iteration only - can be used for testing a newly set up pipeline
+    beekeeper.pl -url mysql://username:secret@hostname:port/long_mult_test -run
+
+        # Reset failed &#39;buggy_analysis&#39; jobs to &#39;READY&#39; state, so that they can be run again
+    beekeeper.pl -url mysql://username:secret@hostname:port/long_mult_test -reset_failed_jobs_for_analysis buggy_analysis
+
+        # Do a cleanup: find and bury dead workers, reclaim their jobs
+    beekeeper.pl -url mysql://username:secret@hostname:port/long_mult_test -dead</code></pre>
+
+<h1 id="OPTIONS">OPTIONS</h1>
+
+<h2 id="Connection-parameters">Connection parameters</h2>
+
+<pre><code>    -reg_conf &lt;path&gt;       : path to a Registry configuration file
+    -reg_type &lt;string&gt;     : type of the registry entry (&#39;hive&#39;, &#39;core&#39;, &#39;compara&#39;, etc - defaults to &#39;hive&#39;)
+    -reg_alias &lt;string&gt;    : species/alias name for the Hive DBAdaptor
+    -url &lt;url string&gt;      : url defining where hive database is located</code></pre>
+
+<h2 id="Looping-control">Looping control</h2>
+
+<pre><code>    -loop                  : run autonomously, loops and sleeps
+    -max_loops &lt;num&gt;       : perform max this # of loops in autonomous mode
+    -keep_alive            : do not stop when there are no more jobs to do - carry on looping
+    -job_id &lt;job_id&gt;       : run 1 iteration for this job_id
+    -run                   : run 1 iteration of automation loop
+    -sleep &lt;num&gt;           : when looping, sleep &lt;num&gt; minutes (default 2min)</code></pre>
+
+<h2 id="Current-Meadow-control">Current Meadow control</h2>
+
+<pre><code>    -meadow_type &lt;string&gt;               : the desired Meadow class name, such as &#39;LSF&#39; or &#39;LOCAL&#39;
+    -total_running_workers_max &lt;num&gt;    : max # workers to be running in parallel
+    -submit_workers_max &lt;num&gt;           : max # workers to create per loop iteration
+    -submission_options &lt;string&gt;        : passes &lt;string&gt; to the Meadow submission command as &lt;options&gt; (formerly lsf_options)
+    -submit_log_dir &lt;dir&gt;               : record submission output+error streams into files under the given directory (to see why some workers fail after submission)</code></pre>
+
+<h2 id="Worker-control">Worker control</h2>
+
+<pre><code>    -job_limit &lt;num&gt;            : #jobs to run before worker can die naturally
+    -life_span &lt;num&gt;            : life_span limit for each worker
+    -logic_name &lt;string&gt;        : restrict the pipeline stat/runs to this analysis logic_name
+    -retry_throwing_jobs 0|1    : if a job dies *knowingly*, should we retry it by default?
+    -can_respecialize &lt;0|1&gt;     : allow workers to re-specialize into another analysis (within resource_class) after their previous analysis was exhausted
+    -hive_log_dir &lt;path&gt;        : directory where stdout/stderr of the hive is redirected
+    -debug &lt;debug_level&gt;        : set debug level of the workers</code></pre>
+
+<h2 id="Other-commands-options">Other commands/options</h2>
+
+<pre><code>    -help                  : print this help
+    -versions              : report both Hive code version and Hive database schema version
+    -dead                  : detect all unaccounted dead workers and reset their jobs for resubmission
+    -alldead               : tell the database all workers are dead (no checks are performed in this mode, so be very careful!)
+    -balance_semaphores    : set all semaphore_counts to the numbers of unDONE fan jobs (emergency use only)
+    -no_analysis_stats     : don&#39;t show status of each analysis
+    -worker_stats          : show status of each running worker
+    -failed_jobs           : show all failed jobs
+    -reset_job_id &lt;num&gt;    : reset a job back to READY so it can be rerun
+    -reset_failed_jobs_for_analysis &lt;logic_name&gt;
+                           : reset FAILED jobs of an analysis back to READY so they can be rerun
+    -reset_all_jobs_for_analysis &lt;logic_name&gt;
+                           : reset ALL jobs of an analysis back to READY so they can be rerun</code></pre>
+
+<h1 id="LICENSE">LICENSE</h1>
+
+<pre><code>    Copyright [1999-2014] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+
+    Licensed under the Apache License, Version 2.0 (the &quot;License&quot;); you may not use this file except in compliance with the License.
+    You may obtain a copy of the License at
+
+         http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing, software distributed under the License
+    is distributed on an &quot;AS IS&quot; 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.</code></pre>
+
+<h1 id="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>
+
+
+</body>
+
+</html>
+
+
--- a/docs/scripts/db_cmd.html
+++ b/docs/scripts/db_cmd.html
+<?xml version="1.0" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title>db_cmd.pl</title>
+<meta http-equiv="content-type" content="text/html; charset=utf-8" />
+<link rev="made" href="mailto:root@localhost" />
+</head>
+
+<body style="background-color: white">
+
+
+
+<h1 id="NAME">NAME</h1>
+
+<pre><code>    db_cmd.pl</code></pre>
+
+<h1 id="SYNOPSIS">SYNOPSIS</h1>
+
+<pre><code>    db_cmd.pl {-url &lt;url&gt; | [-reg_conf &lt;reg_conf&gt;] -reg_alias &lt;reg_alias&gt; [-reg_type &lt;reg_type&gt;] } [ -sql &lt;sql_command&gt; ] [ -extra &lt;extra_params&gt; ] [ -to_params | -verbose ]</code></pre>
+
+<h1 id="DESCRIPTION">DESCRIPTION</h1>
+
+<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>
+
+<h1 id="USAGE-EXAMPLES">USAGE EXAMPLES</h1>
+
+<pre><code>    db_cmd.pl -url &quot;mysql://ensadmin:${ENSADMIN_PSW}@localhost:3306/&quot; -sql &#39;CREATE DATABASE lg4_long_mult&#39;
+    db_cmd.pl -url &quot;mysql://ensadmin:${ENSADMIN_PSW}@localhost:3306/lg4_long_mult&quot;
+    db_cmd.pl -url &quot;mysql://ensadmin:${ENSADMIN_PSW}@localhost:3306/lg4_long_mult&quot; -sql &#39;SELECT * FROM analysis_base&#39; -extra=&#39;--html&#39;
+    eval mysqldump -t `db_cmd.pl -url &quot;mysql://ensadmin:${ENSADMIN_PSW}@localhost:3306/lg4_long_mult&quot; -to_params` worker
+
+    db_cmd.pl -reg_conf ${ENSEMBL_CVS_ROOT_DIR}/ensembl-compara/scripts/pipeline/production_reg_conf.pl -reg_alias compara_master
+    db_cmd.pl -reg_conf ${ENSEMBL_CVS_ROOT_DIR}/ensembl-compara/scripts/pipeline/production_reg_conf.pl -reg_alias mus_musculus   -reg_type core
+    db_cmd.pl -reg_conf ${ENSEMBL_CVS_ROOT_DIR}/ensembl-compara/scripts/pipeline/production_reg_conf.pl -reg_alias squirrel       -reg_type core -sql &#39;SELECT * FROM coord_system&#39;</code></pre>
+
+<h1 id="LICENSE">LICENSE</h1>
+
+<pre><code>    Copyright [1999-2014] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+
+    Licensed under the Apache License, Version 2.0 (the &quot;License&quot;); you may not use this file except in compliance with the License.
+    You may obtain a copy of the License at
+
+         http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing, software distributed under the License
+    is distributed on an &quot;AS IS&quot; 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.</code></pre>
+
+<h1 id="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>
+
+
+</body>
+
+</html>
+
+
--- a/docs/scripts/generate_graph.html
+++ b/docs/scripts/generate_graph.html
+<?xml version="1.0" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title>generate_graph.pl</title>
+<meta http-equiv="content-type" content="text/html; charset=utf-8" />
+<link rev="made" href="mailto:root@localhost" />
+</head>
+
+<body style="background-color: white">
+
+
+
+<h1 id="NAME">NAME</h1>
+
+<pre><code>    generate_graph.pl</code></pre>
+
+<h1 id="SYNOPSIS">SYNOPSIS</h1>
+
+<pre><code>    ./generate_graph.pl -url mysql://user:pass@server:port/dbname -output OUTPUT_LOC [-help]</code></pre>
+
+<h1 id="DESCRIPTION">DESCRIPTION</h1>
+
+<pre><code>    This program will generate a graphical representation of your hive pipeline.
+    This includes visalising the flow of data from the different analyses, blocking
+    rules &amp; table writers. The graph is also coloured to indicate the stage
+    an analysis is at. The colours &amp; fonts used can be configured via
+    hive_config.json configuration file.</code></pre>
+
+<h1 id="OPTIONS">OPTIONS</h1>
+
+<p><b>--url</b></p>
+
+<pre><code>    url defining where hive database is located</code></pre>
+
+<p><b>--reg_conf</b></p>
+
+<pre><code>    path to a Registry configuration file</code></pre>
+
+<p><b>--reg_alias</b></p>
+
+<pre><code>    species/alias name for the Hive DBAdaptor</code></pre>
+
+<p><b>--output</b></p>
+
+<pre><code>    Location of the file to write to.
+    The file extension (.png , .jpeg , .dot , .gif , .ps) will define the output format.</code></pre>
+
+<h1 id="EXTERNAL-DEPENDENCIES">EXTERNAL DEPENDENCIES</h1>
+
+<pre><code>    GraphViz</code></pre>
+
+<h1 id="LICENSE">LICENSE</h1>
+
+<pre><code>    Copyright [1999-2014] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+
+    Licensed under the Apache License, Version 2.0 (the &quot;License&quot;); you may not use this file except in compliance with the License.
+    You may obtain a copy of the License at
+
+         http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing, software distributed under the License
+    is distributed on an &quot;AS IS&quot; 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.</code></pre>
+
+<h1 id="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>
+
+
+</body>
+
+</html>
+
+
--- a/docs/scripts/generate_timeline.html
+++ b/docs/scripts/generate_timeline.html
+<?xml version="1.0" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title>generate_timeline.pl</title>
+<meta http-equiv="content-type" content="text/html; charset=utf-8" />
+<link rev="made" href="mailto:root@localhost" />
+</head>
+
+<body style="background-color: white">
+
+
+
+<h1 id="NAME">NAME</h1>
+
+<pre><code>    generate_timeline.pl</code></pre>
+
+<h1 id="SYNOPSIS">SYNOPSIS</h1>
+
+<pre><code>    generate_timeline.pl {-url &lt;url&gt; | [-reg_conf &lt;reg_conf&gt;] -reg_alias &lt;reg_alias&gt; [-reg_type &lt;reg_type&gt;] }
+                         [-start_date &lt;start_date&gt;] [-end_date &lt;end_date&gt;]
+                         [-top &lt;float&gt;]
+                         [-mode [workers | memory | cores | unused_memory | unused_cores | pending_workers]]
+                         [-n_core &lt;int&gt;] [-mem &lt;int&gt;]</code></pre>
+
+<h1 id="DESCRIPTION">DESCRIPTION</h1>
+
+<pre><code>    This script is used for offline examination of the allocation of workers.
+
+    Based on the command-line parameters &#39;start_date&#39; and &#39;end_date&#39;, 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 &#39;worker&#39; table for accurate timing.
+    By default, the output is in CSV format, to allow extra analysis to be carried.
+
+    You can optionally ask the script to generate an image with Gnuplot.</code></pre>
+
+<h1 id="USAGE-EXAMPLES">USAGE EXAMPLES</h1>
+
+<pre><code>        # Just run it the usual way: only the top 20 analysis will be reported in CSV format
+    generate_timeline.pl -url mysql://username:secret@hostname:port/database &gt; timeline.csv
+
+        # The same, but getting the analysis that fill 99.5% of the global activity in a PNG file
+    generate_timeline.pl -url mysql://username:secret@hostname:port/database -top .995 -output timeline_top995.png
+
+        # Assuming you are only interested in a precise interval (in a PNG file)
+    generate_timeline.pl -url mysql://username:secret@hostname:port/database -start_date 2013-06-15T10:34 -end_date 2013-06-15T16:58 -output timeline_June15.png
+
+        # Get the required memory instead of the number of workers
+    generate_timeline.pl -url mysql://username:secret@hostname:port/database -mode memory -output timeline_memory.png</code></pre>
+
+<h1 id="OPTIONS">OPTIONS</h1>
+
+<pre><code>    -help                   : print this help
+    -url &lt;url string&gt;       : url defining where hive database is located
+    -reg_cong, -reg_type, -reg_alias    : alternative connection details
+    -nosqlvc                : Do not restrict the usage of this script to the current version of eHive
+                              Be aware that generate_timeline.pl uses raw SQL queries that may break on different schema versions
+    -verbose                : Print some info about the data loaded from the database
+
+    -start_date &lt;date&gt;      : minimal start date of a worker (the format is ISO8601, e.g. &#39;2012-01-25T13:46&#39;)
+    -end_date &lt;date&gt;        : maximal end date of a worker (the format is ISO8601, e.g. &#39;2012-01-25T13:46&#39;)
+    -top &lt;float&gt;            : maximum number (&gt; 1) or fraction (&lt; 1) of analysis to report (default: 20)
+    -output &lt;string&gt;        : output file: its extension must match one of the Gnuplot terminals. Otherwise, the CSV output is produced on stdout
+    -mode &lt;string&gt;          : what should be displayed on the y-axis. Allowed values are &#39;workers&#39; (default), &#39;memory&#39;, &#39;cores&#39;, &#39;unused_memory&#39;, &#39;unused_cores&#39;, &#39;pending_workers&#39;
+
+    -n_core &lt;int&gt;           : the default number of cores allocated to a worker (default: 1)
+    -mem &lt;int&gt;              : the default memory allocated to a worker (default: 100Mb)</code></pre>
+
+<h1 id="EXTERNAL-DEPENDENCIES">EXTERNAL DEPENDENCIES</h1>
+
+<pre><code>    Chart::Gnuplot</code></pre>
+
+<h1 id="LICENSE">LICENSE</h1>
+
+<pre><code>    Copyright [1999-2014] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+
+    Licensed under the Apache License, Version 2.0 (the &quot;License&quot;); you may not use this file except in compliance with the License.
+    You may obtain a copy of the License at
+
+         http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing, software distributed under the License
+    is distributed on an &quot;AS IS&quot; 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.</code></pre>
+
+<h1 id="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>
+
+
+</body>
+
+</html>
+
+
--- a/docs/scripts/hoover_pipeline.html
+++ b/docs/scripts/hoover_pipeline.html
+<?xml version="1.0" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title>hoover_pipeline.pl</title>
+<meta http-equiv="content-type" content="text/html; charset=utf-8" />
+<link rev="made" href="mailto:root@localhost" />
+</head>
+
+<body style="background-color: white">
+
+
+
+<h1 id="NAME">NAME</h1>
+
+<pre><code>    hoover_pipeline.pl</code></pre>
+
+<h1 id="SYNOPSIS">SYNOPSIS</h1>
+
+<pre><code>    hoover_pipeline.pl {-url &lt;url&gt; | -reg_conf &lt;reg_conf&gt; -reg_alias &lt;reg_alias&gt;} [ { -before_datetime &lt;datetime&gt; | -days_ago &lt;days_ago&gt; } ]</code></pre>
+
+<h1 id="DESCRIPTION">DESCRIPTION</h1>
+
+<pre><code>    hoover_pipeline.pl is a script used to remove old &#39;DONE&#39; jobs from a continuously running pipeline database</code></pre>
+
+<h1 id="USAGE-EXAMPLES">USAGE EXAMPLES</h1>
+
+<pre><code>        # delete all jobs that have been &#39;DONE&#39; for at least a week (default threshold) :
+
+    hoover_pipeline.pl -url &quot;mysql://ensadmin:${ENSADMIN_PSW}@localhost:3306/lg4_long_mult&quot;
+
+
+        # delete all jobs that have been &#39;DONE&#39; for at least a given number of days
+
+    hoover_pipeline.pl -url &quot;mysql://ensadmin:${ENSADMIN_PSW}@localhost:3306/lg4_long_mult&quot; -days_ago 3
+
+
+        # delete all jobs &#39;DONE&#39; before a specific datetime:
+
+    hoover_pipeline.pl -url &quot;mysql://ensadmin:${ENSADMIN_PSW}@localhost:3306/lg4_long_mult&quot; -before_datetime &quot;2013-02-14 15:42:50&quot;</code></pre>
+
+<h1 id="LICENSE">LICENSE</h1>
+
+<pre><code>    Copyright [1999-2014] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+
+    Licensed under the Apache License, Version 2.0 (the &quot;License&quot;); you may not use this file except in compliance with the License.
+    You may obtain a copy of the License at
+
+         http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing, software distributed under the License
+    is distributed on an &quot;AS IS&quot; 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.</code></pre>
+
+<h1 id="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>
+
+
+</body>
+
+</html>
+
+
--- a/docs/scripts/index.html
+++ b/docs/scripts/index.html
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
+<html>
+<head>
+ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+ <meta name="Author" content="Made by 'tree'">
+ <meta name="GENERATOR" content="$Version: $ tree v1.6.0 (c) 1996 - 2011 by Steve Baker, Thomas Moore, Francesc Rocher, Kyosuke Tokoro $">
+ <title>eHive 1.9 scripts</title>
+ <style type="text/css">
+  <!-- 
+  BODY { font-family : ariel, monospace, sans-serif; }
+  P { font-weight: normal; font-family : ariel, monospace, sans-serif; color: black; background-color: transparent;}
+  B { font-weight: normal; color: black; background-color: transparent;}
+  A:visited { font-weight : normal; text-decoration : none; background-color : transparent; margin : 0px 0px 0px 0px; padding : 0px 0px 0px 0px; display: inline; }
+  A:link    { font-weight : normal; text-decoration : none; margin : 0px 0px 0px 0px; padding : 0px 0px 0px 0px; display: inline; }
+  A:hover   { color : #000000; font-weight : normal; text-decoration : underline; background-color : yellow; margin : 0px 0px 0px 0px; padding : 0px 0px 0px 0px; display: inline; }
+  A:active  { color : #000000; font-weight: normal; background-color : transparent; margin : 0px 0px 0px 0px; padding : 0px 0px 0px 0px; display: inline; }
+  .VERSION { font-size: small; font-family : arial, sans-serif; }
+  .NORM  { color: black;  background-color: transparent;}
+  .FIFO  { color: purple; background-color: transparent;}
+  .CHAR  { color: yellow; background-color: transparent;}
+  .DIR   { color: blue;   background-color: transparent;}
+  .BLOCK { color: yellow; background-color: transparent;}
+  .LINK  { color: aqua;   background-color: transparent;}
+  .SOCK  { color: fuchsia;background-color: transparent;}
+  .EXEC  { color: green;  background-color: transparent;}
+  -->
+ </style>
+</head>
+<body>
+	<h1>eHive 1.9 scripts</h1><p>
+	<a href=".">.</a><br>
+	├── <a href="./beekeeper.html">beekeeper.html</a><br>
+	├── <a href="./db_cmd.html">db_cmd.html</a><br>
+	├── <a href="./generate_graph.html">generate_graph.html</a><br>
+	├── <a href="./generate_timeline.html">generate_timeline.html</a><br>
+	├── <a href="./hoover_pipeline.html">hoover_pipeline.html</a><br>
+	├── <a href="./index.html">index.html</a><br>
+	├── <a href="./init_pipeline.html">init_pipeline.html</a><br>
+	├── <a href="./lsf_report.html">lsf_report.html</a><br>
+	├── <a href="./runWorker.html">runWorker.html</a><br>
+	├── <a href="./seed_pipeline.html">seed_pipeline.html</a><br>
+	└── <a href="./standaloneJob.html">standaloneJob.html</a><br>
+	<br><br>
+	</p>
+	<p>
+
+0 directories, 11 files
+	<br><br>
+	</p>
+	<hr>
+	<p class="VERSION">
+		 tree v1.6.0 © 1996 - 2011 by Steve Baker and Thomas Moore <br>
+		 HTML output hacked and copyleft © 1998 by Francesc Rocher <br>
+		 Charsets / OS/2 support © 2001 by Kyosuke Tokoro
+	</p>
+</body>
+</html>
--- a/docs/scripts/init_pipeline.html
+++ b/docs/scripts/init_pipeline.html
+<?xml version="1.0" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title>init_pipeline.pl</title>
+<meta http-equiv="content-type" content="text/html; charset=utf-8" />
+<link rev="made" href="mailto:root@localhost" />
+</head>
+
+<body style="background-color: white">
+
+
+
+<h1 id="NAME">NAME</h1>
+
+<pre><code>    init_pipeline.pl</code></pre>
+
+<h1 id="SYNOPSIS">SYNOPSIS</h1>
+
+<pre><code>    init_pipeline.pl &lt;config_module_or_filename&gt; [-help | [-analysis_topup | -job_topup] &lt;options_for_this_particular_pipeline&gt;]</code></pre>
+
+<h1 id="DESCRIPTION">DESCRIPTION</h1>
+
+<pre><code>    init_pipeline.pl is a generic script that is used to create+setup=initialize eHive pipelines from PipeConfig configuration modules.</code></pre>
+
+<h1 id="USAGE-EXAMPLES">USAGE EXAMPLES</h1>
+
+<pre><code>        # get this help message:
+    init_pipeline.pl
+
+        # initialize a generic eHive pipeline:
+    init_pipeline.pl Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf -password &lt;yourpassword&gt;
+
+        # see what command line options are available when initializing long multiplication example pipeline
+        #   (assuming your current directory is ensembl-hive/modules/Bio/EnsEMBL/Hive) :
+    init_pipeline.pl PipeConfig/LongMult_conf -help
+
+        # initialize the long multiplicaton pipeline by supplying not only mandatory but also optional data:
+        #   (assuming your current directory is ensembl-hive/modules/Bio/EnsEMBL/Hive/PipeConfig) :
+    init_pipeline.pl LongMult_conf -password &lt;yourpassword&gt; -first_mult 375857335 -second_mult 1111333355556666 </code></pre>
+
+<h1 id="OPTIONS">OPTIONS</h1>
+
+<pre><code>    -help            :   Gets this help message and exits
+
+    -analysis_topup  :   A special initialization mode when (1) pipeline_create_commands are switched off and (2) only newly defined analyses are added to the database
+                         This mode is only useful in the process of putting together a new pipeline.
+
+    -job_topup       :   Another special initialization mode when only jobs are created - no other structural changes to the pipeline are acted upon.
+
+    -hive_force_init :   If set to 1, forces the (re)creation of the hive database even if a previous version of it is present in the server.</code></pre>
+
+<h1 id="LICENSE">LICENSE</h1>
+
+<pre><code>    Copyright [1999-2014] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+
+    Licensed under the Apache License, Version 2.0 (the &quot;License&quot;); you may not use this file except in compliance with the License.
+    You may obtain a copy of the License at
+
+         http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing, software distributed under the License
+    is distributed on an &quot;AS IS&quot; 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.</code></pre>
+
+<h1 id="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>
+
+
+</body>
+
+</html>
+
+
--- a/docs/scripts/lsf_report.html
+++ b/docs/scripts/lsf_report.html
+<?xml version="1.0" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title>lsf_report.pl</title>
+<meta http-equiv="content-type" content="text/html; charset=utf-8" />
+<link rev="made" href="mailto:root@localhost" />
+</head>
+
+<body style="background-color: white">
+
+
+
+<h1 id="NAME">NAME</h1>
+
+<pre><code>    lsf_report.pl</code></pre>
+
+<h1 id="DESCRIPTION">DESCRIPTION</h1>
+
+<pre><code>    This script is used for offline examination of resources used by a Hive pipeline running on LSF
+    (the script is [Pp]latform-dependent).
+
+    Based on the command-line parameters &#39;start_date&#39; and &#39;end_date&#39;, 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 LSF&#39;s &#39;bacct&#39; database, parses it and stores in &#39;lsf_report&#39; table.
+    You can join this table to &#39;worker&#39; table USING(meadow_name,process_id) in the usual MySQL way
+    to filter by analysis_id, do various stats, etc.
+
+    You can optionally ask the script to dump the &#39;bacct&#39; database in a dump file,
+    or fill in the &#39;lsf_report&#39; table from an existing dump file (most time is taken by querying bacct).
+
+    Please note the script may additionally pull information about LSF processes that you ran simultaneously
+    with running the pipeline. It is easy to ignore them by joining into &#39;worker&#39; table.</code></pre>
+
+<h1 id="USAGE-EXAMPLES">USAGE EXAMPLES</h1>
+
+<pre><code>        # Just run it the usual way: query &#39;bacct&#39; and load the relevant data into &#39;lsf_report&#39; table:
+    lsf_report.pl -url mysql://username:secret@hostname:port/long_mult_test
+
+        # The same, but assuming LSF user someone_else ran the pipeline:
+    lsf_report.pl -url mysql://username:secret@hostname:port/long_mult_test -lsf_user someone_else
+
+        # Assuming the dump file existed. Load the dumped bacct data into &#39;lsf_report&#39; table:
+    lsf_report.pl -url mysql://username:secret@hostname:port/long_mult_test -dump long_mult.bacct
+
+        # Assuming the dump file did not exist. Query &#39;bacct&#39;, dump the data into a file and load it into &#39;lsf_report&#39;:
+    lsf_report.pl -url mysql://username:secret@hostname:port/long_mult_test -dump long_mult_again.bacct</code></pre>
+
+<h1 id="OPTIONS">OPTIONS</h1>
+
+<pre><code>    -help                   : print this help
+    -url &lt;url string&gt;       : url defining where hive database is located
+    -dump &lt;filename&gt;        : a filename for bacct dump. It will be read from if the file exists, and written to otherwise.
+    -lsf_user &lt;username&gt;    : if it wasn&#39;t you who ran the pipeline, LSF user name of that user can be provided
+    -start_date &lt;date&gt;      : minimal start date of a job (the format is &#39;2012/01/25/13:46&#39;)
+    -end_date &lt;date&gt;        : maximal end date of a job (the format is &#39;2012/01/25/13:46&#39;)</code></pre>
+
+<h1 id="LICENSE">LICENSE</h1>
+
+<pre><code>    Copyright [1999-2014] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+
+    Licensed under the Apache License, Version 2.0 (the &quot;License&quot;); you may not use this file except in compliance with the License.
+    You may obtain a copy of the License at
+
+         http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing, software distributed under the License
+    is distributed on an &quot;AS IS&quot; 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.</code></pre>
+
+<h1 id="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>
+
+
+</body>
+
+</html>
+
+
--- a/docs/scripts/runWorker.html
+++ b/docs/scripts/runWorker.html
+<?xml version="1.0" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title>runWorker.pl</title>
+<meta http-equiv="content-type" content="text/html; charset=utf-8" />
+<link rev="made" href="mailto:root@localhost" />
+</head>
+
+<body style="background-color: white">
+
+
+
+<h1 id="NAME">NAME</h1>
+
+<pre><code>    runWorker.pl</code></pre>
+
+<h1 id="DESCRIPTION">DESCRIPTION</h1>
+
+<pre><code>    runWorker.pl is an eHive component script that does the work of a single Worker -
+    specializes in one of the analyses and starts executing jobs of that analysis one-by-one or batch-by-batch.
+
+    Most of the functionality of the eHive is accessible via beekeeper.pl script,
+    but feel free to run the runWorker.pl if you think you know what you are doing :)</code></pre>
+
+<h1 id="USAGE-EXAMPLES">USAGE EXAMPLES</h1>
+
+<pre><code>        # Run one local worker process in ehive_dbname and let the system pick up the analysis
+    runWorker.pl -url mysql://username:secret@hostname:port/ehive_dbname
+
+        # Run one local worker process in ehive_dbname and let the system pick up the analysis from the given resource_class
+    runWorker.pl -url mysql://username:secret@hostname:port/ehive_dbname -rc_name low_mem
+
+        # Run one local worker process in ehive_dbname and specify the logic_name
+    runWorker.pl -url mysql://username:secret@hostname:port/ehive_dbname -logic_name fast_blast
+
+        # Run a specific job in a local worker process:
+    runWorker.pl -url mysql://username:secret@hostname:port/ehive_dbname -job_id 123456</code></pre>
+
+<h1 id="OPTIONS">OPTIONS</h1>
+
+<h2 id="Connection-parameters">Connection parameters:</h2>
+
+<pre><code>    -reg_conf &lt;path&gt;        : path to a Registry configuration file
+    -reg_alias &lt;string&gt;     : species/alias name for the Hive DBAdaptor
+    -url &lt;url string&gt;       : url defining where database is located</code></pre>
+
+<h2 id="Task-specificaton-parameters">Task specificaton parameters:</h2>
+
+<pre><code>    -rc_id &lt;id&gt;                 : resource class id
+    -rc_name &lt;string&gt;           : resource class name
+    -analysis_id &lt;id&gt;           : pre-specify this worker in a particular analysis defined by database id
+    -logic_name &lt;string&gt;        : pre-specify this worker in a particular analysis defined by name
+    -job_id &lt;id&gt;                : run a specific job defined by its database id
+    -force 0|1                  : set to 1 if you want to force running a Worker over a BLOCKED analysis or to run a specific DONE/SEMAPHORED job_id</code></pre>
+
+<h2 id="Worker-control-parameters">Worker control parameters:</h2>
+
+<pre><code>    -job_limit &lt;num&gt;            : #jobs to run before worker can die naturally
+    -life_span &lt;num&gt;            : number of minutes this worker is allowed to run
+    -no_cleanup                 : don&#39;t perform temp directory cleanup when worker exits
+    -no_write                   : don&#39;t write_output or auto_dataflow input_job
+    -hive_log_dir &lt;path&gt;        : directory where stdout/stderr of the whole hive of workers is redirected
+    -worker_log_dir &lt;path&gt;      : directory where stdout/stderr of this particular worker is redirected
+    -retry_throwing_jobs &lt;0|1&gt;  : if a job dies *knowingly*, should we retry it by default?
+    -can_respecialize &lt;0|1&gt;     : allow this worker to re-specialize into another analysis (within resource_class) after it has exhausted all jobs of the current one</code></pre>
+
+<h2 id="Other-options">Other options:</h2>
+
+<pre><code>    -help                       : print this help
+    -versions                   : report both Hive code version and Hive database schema version
+    -debug &lt;level&gt;              : turn on debug messages at &lt;level&gt;
+    -analysis_stats             : show status of each analysis in hive</code></pre>
+
+<h1 id="LICENSE">LICENSE</h1>
+
+<pre><code>    Copyright [1999-2014] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+
+    Licensed under the Apache License, Version 2.0 (the &quot;License&quot;); you may not use this file except in compliance with the License.
+    You may obtain a copy of the License at
+
+         http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing, software distributed under the License
+    is distributed on an &quot;AS IS&quot; 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.</code></pre>
+
+<h1 id="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>
+
+
+</body>
+
+</html>
+
+
--- a/docs/scripts/seed_pipeline.html
+++ b/docs/scripts/seed_pipeline.html
+<?xml version="1.0" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title>seed_pipeline.pl</title>
+<meta http-equiv="content-type" content="text/html; charset=utf-8" />
+<link rev="made" href="mailto:root@localhost" />
+</head>
+
+<body style="background-color: white">
+
+
+
+<h1 id="NAME">NAME</h1>
+
+<pre><code>    seed_pipeline.pl</code></pre>
+
+<h1 id="SYNOPSIS">SYNOPSIS</h1>
+
+<pre><code>    seed_pipeline.pl {-url &lt;url&gt; | -reg_conf &lt;reg_conf&gt; [-reg_type &lt;reg_type&gt;] -reg_alias &lt;reg_alias&gt;} [ {-analysis_id &lt;analysis_id&gt; | -logic_name &lt;logic_name&gt;} [ -input_id &lt;input_id&gt; ] ]</code></pre>
+
+<h1 id="DESCRIPTION">DESCRIPTION</h1>
+
+<pre><code>    seed_pipeline.pl is a generic script that is used to create {initial or top-up} jobs for hive pipelines</code></pre>
+
+<h1 id="USAGE-EXAMPLES">USAGE EXAMPLES</h1>
+
+<pre><code>        # find out which analyses may need seeding (with an example input_id):
+
+    seed_pipeline.pl -url &quot;mysql://ensadmin:${ENSADMIN_PSW}@localhost:3306/lg4_long_mult&quot;
+
+
+        # seed one job into the &quot;start&quot; analysis:
+
+    seed_pipeline.pl -url &quot;mysql://ensadmin:${ENSADMIN_PSW}@localhost:3306/lg4_long_mult&quot; \
+                     -logic_name start -input_id &#39;{&quot;a_multiplier&quot; =&gt; 2222222222, &quot;b_multiplier&quot; =&gt; 3434343434}&#39;</code></pre>
+
+<h1 id="LICENSE">LICENSE</h1>
+
+<pre><code>    Copyright [1999-2014] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+
+    Licensed under the Apache License, Version 2.0 (the &quot;License&quot;); you may not use this file except in compliance with the License.
+    You may obtain a copy of the License at
+
+         http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing, software distributed under the License
+    is distributed on an &quot;AS IS&quot; 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.</code></pre>
+
+<h1 id="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>
+
+
+</body>
+
+</html>
+
+
--- a/docs/scripts/standaloneJob.html
+++ b/docs/scripts/standaloneJob.html
+<?xml version="1.0" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title>standaloneJob.pl</title>
+<meta http-equiv="content-type" content="text/html; charset=utf-8" />
+<link rev="made" href="mailto:root@localhost" />
+</head>
+
+<body style="background-color: white">
+
+
+
+<h1 id="NAME">NAME</h1>
+
+<pre><code>    standaloneJob.pl</code></pre>
+
+<h1 id="DESCRIPTION">DESCRIPTION</h1>
+
+<pre><code>    standaloneJob.pl is an eHive component script that
+        1. takes in a RunnableDB module,
+        2. creates a standalone job outside an eHive database by initializing parameters from command line arguments (ARRAY- and HASH- arguments can be passed+parsed too!)
+        3. and runs that job outside the database.
+        4. can optionally dataflow into tables fully defined by URLs
+    Naturally, only certain RunnableDB modules can be run using this script, and some database-related functionality will be lost.</code></pre>
+
+<h1 id="USAGE-EXAMPLES">USAGE EXAMPLES</h1>
+
+<pre><code>        # Run a job with default parameters, specify module by its package name:
+    standaloneJob.pl Bio::EnsEMBL::Hive::RunnableDB::FailureTest
+
+        # Run the same job with default parameters, but specify module by its relative filename:
+    standaloneJob.pl RunnableDB/FailureTest.pm
+
+        # Run a job and re-define some of the default parameters:
+    standaloneJob.pl Bio::EnsEMBL::Hive::RunnableDB::FailureTest -time_RUN=2 -time_WRITE_OUTPUT=3 -state=WRITE_OUTPUT -value=2
+    standaloneJob.pl Bio::EnsEMBL::Hive::RunnableDB::SystemCmd -cmd &#39;ls -l&#39;
+    standaloneJob.pl Bio::EnsEMBL::Hive::RunnableDB::SystemCmd -input_id &quot;{ &#39;cmd&#39; =&gt; &#39;ls -l&#39; }&quot;
+
+        # Run a job and re-define its &#39;db_conn&#39; parameter to allow it to perform some database-related operations:
+    standaloneJob.pl RunnableDB/SqlCmd.pm -db_conn mysql://ensadmin:xxxxxxx@127.0.0.1:2912/lg4_compara_families_63 -sql &#39;INSERT INTO meta (meta_key,meta_value) VALUES (&quot;hello&quot;, &quot;world2&quot;)&#39;
+
+        # Run a job with given parameters, but skip the write_output() step:
+    standaloneJob.pl Bio::EnsEMBL::Hive::RunnableDB::FailureTest -no_write -time_RUN=2 -time_WRITE_OUTPUT=3 -state=WRITE_OUTPUT -value=2
+
+        # Run a job and re-direct its dataflow into tables:
+    standaloneJob.pl Bio::EnsEMBL::Hive::RunnableDB::JobFactory -inputfile foo.txt -delimiter &#39;\t&#39; -column_names &quot;[ &#39;name&#39;, &#39;age&#39; ]&quot; \
+                        -flow_into &quot;{ 2 =&gt; [&#39;mysql://ensadmin:xxxxxxx@127.0.0.1:2914/lg4_triggers/foo&#39;, &#39;mysql://ensadmin:xxxxxxx@127.0.0.1:2914/lg4_triggers/bar&#39;] }&quot;
+
+        # Run a Compara job that needs a connection to Compara database:
+    standaloneJob.pl Bio::EnsEMBL::Compara::RunnableDB::ObjectFactory -compara_db &#39;mysql://ensadmin:xxxxxxx@127.0.0.1:2911/sf5_ensembl_compara_master&#39; \
+                        -adaptor_name MethodLinkSpeciesSetAdaptor -adaptor_method fetch_all_by_method_link_type -method_param_list &quot;[ &#39;ENSEMBL_ORTHOLOGUES&#39; ]&quot; \
+                        -column_names2getters &quot;{ &#39;name&#39; =&gt; &#39;name&#39;, &#39;mlss_id&#39; =&gt; &#39;dbID&#39; }&quot; -flow_into &quot;{ 2 =&gt; &#39;mysql://ensadmin:xxxxxxx@127.0.0.1:2914/lg4_triggers/baz&#39; }&quot;
+
+        # Create a new job in a database using automatic dataflow from a database-less Dummy job:
+    standaloneJob.pl Bio::EnsEMBL::Hive::RunnableDB::Dummy -a_multiplier 1234567 -b_multiplier 9876543 \
+                        -flow_into &quot;{ 1 =&gt; &#39;mysql://ensadmin:xxxxxxx@127.0.0.1/lg4_long_mult/analysis?logic_name=start&#39; }&quot;</code></pre>
+
+<h1 id="SCRIPT-SPECIFIC-OPTIONS">SCRIPT-SPECIFIC OPTIONS</h1>
+
+<pre><code>    -help               : print this help
+    -debug &lt;level&gt;      : turn on debug messages at &lt;level&gt;
+    -no_write           : skip the execution of write_output() step this time
+    -reg_conf &lt;path&gt;    : load registry entries from the given file (these entries may be needed by the RunnableDB itself)
+    -input_id &quot;&lt;hash&gt;&quot;  : specify the whole input_id parameter in one stringified hash
+    -flow_out &quot;&lt;hash&gt;&quot;  : defines the dataflow re-direction rules in a format similar to PipeConfig&#39;s - see the last example
+
+    NB: all other options will be passed to the runnable (leading dashes removed) and will constitute the parameters for the job.</code></pre>
+
+<h1 id="LICENSE">LICENSE</h1>
+
+<pre><code>    Copyright [1999-2014] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+
+    Licensed under the Apache License, Version 2.0 (the &quot;License&quot;); you may not use this file except in compliance with the License.
+    You may obtain a copy of the License at
+
+         http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing, software distributed under the License
+    is distributed on an &quot;AS IS&quot; 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.</code></pre>
+
+<h1 id="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>
+
+
+</body>
+
+</html>
+
+