Commit 8cfd4667 authored by Matthieu Muffato's avatar Matthieu Muffato
Browse files

Regenerated the scripts documentation using a recent toolchain

parent ae1af66f
......@@ -4,170 +4,124 @@
<head>
<title>beekeeper.pl</title>
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<link rev="made" href="mailto:_mdnsresponder@scream.apple.com" />
<link rev="made" href="mailto:root@localhost" />
</head>
<body style="background-color: white">
<body>
<!-- INDEX BEGIN -->
<div name="index">
<p><a name="__index__"></a></p>
<!--
<ul>
<h1 id="NAME">NAME</h1>
<li><a href="#name">NAME</a></li>
<li><a href="#description">DESCRIPTION</a></li>
<li><a href="#usage_examples">USAGE EXAMPLES</a></li>
<li><a href="#options">OPTIONS</a></li>
<ul>
<pre><code> beekeeper.pl [options]</code></pre>
<li><a href="#connection_parameters">Connection parameters</a></li>
<li><a href="#configs_overriding">Configs overriding</a></li>
<li><a href="#looping_control">Looping control</a></li>
<li><a href="#current_meadow_control">Current Meadow control</a></li>
<li><a href="#worker_control">Worker control</a></li>
<li><a href="#other_commands_options">Other commands/options</a></li>
</ul>
<h1 id="DESCRIPTION">DESCRIPTION</h1>
<li><a href="#license">LICENSE</a></li>
<li><a href="#contact">CONTACT</a></li>
</ul>
<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>
</div>
<!-- INDEX END -->
<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
<p>
</p>
<hr />
<h1><a name="name">NAME</a></h1>
<pre>
beekeeper.pl [options]</pre>
<p>
</p>
<hr />
<h1><a name="description">DESCRIPTION</a></h1>
<pre>
The Beekeeper is in charge of interfacing between the Queen and a compute resource or 'compute farm'.
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.</pre>
<pre>
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.</pre>
<p>
</p>
<hr />
<h1><a name="usage_examples">USAGE EXAMPLES</a></h1>
<pre>
# 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</pre>
<pre>
# 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</pre>
<pre>
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</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
beekeeper.pl -url mysql://username:secret@hostname:port/long_mult_test -analyses_pattern 'blast%-4..6' -loop</pre>
<pre>
beekeeper.pl -url mysql://username:secret@hostname:port/long_mult_test -analyses_pattern &#39;blast%-4..6&#39; -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</pre>
<pre>
# Reset failed 'buggy_analysis' jobs to 'READY' state, so that they can be run again
beekeeper.pl -url mysql://username:secret@hostname:port/long_mult_test -analyses_pattern buggy_analysis -reset_failed_jobs</pre>
<pre>
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 -analyses_pattern buggy_analysis -reset_failed_jobs
# Do a cleanup: find and bury dead workers, reclaim their jobs
beekeeper.pl -url mysql://username:secret@hostname:port/long_mult_test -dead</pre>
<p>
</p>
<hr />
<h1><a name="options">OPTIONS</a></h1>
<p>
</p>
<h2><a name="connection_parameters">Connection parameters</a></h2>
<pre>
-reg_conf &lt;path&gt; : path to a Registry configuration file
-reg_type &lt;string&gt; : type of the registry entry ('hive', 'core', 'compara', etc - defaults to 'hive')
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</pre>
<p>
</p>
<h2><a name="configs_overriding">Configs overriding</a></h2>
<pre>
-config_file &lt;string&gt; : json file (with absolute path) to override the default configurations (could be multiple)</pre>
<p>
</p>
<h2><a name="looping_control">Looping control</a></h2>
<pre>
-loop : run autonomously, loops and sleeps
-url &lt;url string&gt; : url defining where hive database is located</code></pre>
<h2 id="Configs-overriding">Configs overriding</h2>
<pre><code> -config_file &lt;string&gt; : json file (with absolute path) to override the default configurations (could be multiple)</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 1 min)</pre>
<p>
</p>
<h2><a name="current_meadow_control">Current Meadow control</a></h2>
<pre>
-meadow_type &lt;string&gt; : the desired Meadow class name, such as 'LSF' or 'LOCAL'
-sleep &lt;num&gt; : when looping, sleep &lt;num&gt; minutes (default 1 min)</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)</pre>
<p>
</p>
<h2><a name="worker_control">Worker control</a></h2>
<pre>
-analyses_pattern &lt;string&gt; : restrict the sync operation, printing of stats or looping of the beekeeper to the specified subset of analyses
-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> -analyses_pattern &lt;string&gt; : restrict the sync operation, printing of stats or looping of the beekeeper to the specified subset of analyses
-can_respecialize &lt;0|1&gt; : allow workers to re-specialize into another analysis (within resource_class) after their previous analysis was exhausted
-life_span &lt;num&gt; : life_span limit for each worker
-life_span &lt;num&gt; : number of minutes each worker is allowed to run
-job_limit &lt;num&gt; : #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 &lt;path&gt; : directory where stdout/stderr of the hive is redirected
-debug &lt;debug_level&gt; : set debug level of the workers</pre>
<p>
</p>
<h2><a name="other_commands_options">Other commands/options</a></h2>
<pre>
-help : print this help
-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't show status of each analysis
-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 : reset FAILED jobs of -analyses_filter'ed ones back to READY so they can be rerun
-reset_all_jobs : reset ALL jobs of -analyses_filter'ed ones back to READY so they can be rerun</pre>
<p>
</p>
<hr />
<h1><a name="license">LICENSE</a></h1>
<pre>
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2020] EMBL-European Bioinformatics Institute</pre>
<pre>
-reset_failed_jobs : reset FAILED jobs of analyses matching -analyses_pattern back to READY so they can be rerun
-reset_all_jobs : reset ALL jobs of analyses matching -analyses_pattern back to READY so they can be rerun</code></pre>
<h1 id="LICENSE">LICENSE</h1>
<pre><code> Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2020] 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</pre>
<pre>
<a href="http://www.apache.org/licenses/LICENSE-2.0">http://www.apache.org/licenses/LICENSE-2.0</a></pre>
<pre>
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.</pre>
<p>
</p>
<hr />
<h1><a name="contact">CONTACT</a></h1>
<pre>
Please subscribe to the Hive mailing list: <a href="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>
<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>
......@@ -4,88 +4,58 @@
<head>
<title>db_cmd.pl</title>
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<link rev="made" href="mailto:_mdnsresponder@scream.apple.com" />
<link rev="made" href="mailto:root@localhost" />
</head>
<body style="background-color: white">
<!-- INDEX BEGIN -->
<div name="index">
<p><a name="__index__"></a></p>
<!--
<ul>
<li><a href="#name">NAME</a></li>
<li><a href="#synopsis">SYNOPSIS</a></li>
<li><a href="#description">DESCRIPTION</a></li>
<li><a href="#usage_examples">USAGE EXAMPLES</a></li>
<li><a href="#license">LICENSE</a></li>
<li><a href="#contact">CONTACT</a></li>
</ul>
-->
</div>
<!-- INDEX END -->
<p>
</p>
<hr />
<h1><a name="name">NAME</a></h1>
<pre>
db_cmd.pl</pre>
<p>
</p>
<hr />
<h1><a name="synopsis">SYNOPSIS</a></h1>
<pre>
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;] } [ -exec &lt;alt_executable&gt; ] [ -prepend &lt;prepend_params&gt; ] [ -append &lt;append_params&gt; ] [ -sql &lt;sql_command&gt; ] [ -to_params | -verbose ]</pre>
<p>
</p>
<hr />
<h1><a name="description">DESCRIPTION</a></h1>
<pre>
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.</pre>
<p>
</p>
<hr />
<h1><a name="usage_examples">USAGE EXAMPLES</a></h1>
<pre>
db_cmd.pl -url &quot;mysql://ensadmin:${ENSADMIN_PSW}@localhost:3306/&quot; -sql 'CREATE DATABASE lg4_long_mult'
<body>
<h1 id="NAME">NAME</h1>
<pre><code> db_cmd.pl</code></pre>
<h1 id="SYNOPSIS">SYNOPSIS</h1>
<pre><code> db_cmd.pl {-url &lt;url&gt; | [-reg_conf &lt;reg_conf&gt;] -reg_alias &lt;reg_alias&gt; [-reg_type &lt;reg_type&gt;] } [ -exec &lt;alt_executable&gt; ] [ -prepend &lt;prepend_params&gt; ] [ -append &lt;append_params&gt; ] [ -sql &lt;sql_command&gt; ] [ -to_params | -verbose ]</code></pre>
<h1 id="DESCRIPTION">DESCRIPTION</h1>
<pre><code> db_cmd.pl is a generic script that connects you interactively to your database using either URL or Registry and optionally runs an SQL command.
-url is exclusive to -reg_alias. -reg_type is only needed if several databases map to that alias / species.</code></pre>
<h1 id="USAGE-EXAMPLES">USAGE EXAMPLES</h1>
<pre><code> db_cmd.pl -url &quot;mysql://ensadmin:${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 'SELECT * FROM analysis_base' -append='--html'
db_cmd.pl -url &quot;mysql://ensadmin:${ENSADMIN_PSW}@localhost/lg4_long_mult&quot; -exec mysqldump -prepend -t -append analysis_base -append job</pre>
<pre>
db_cmd.pl -url &quot;mysql://ensadmin:${ENSADMIN_PSW}@localhost:3306/lg4_long_mult&quot; -sql &#39;SELECT * FROM analysis_base&#39; -append=&#39;--html&#39;
db_cmd.pl -url &quot;mysql://ensadmin:${ENSADMIN_PSW}@localhost/lg4_long_mult&quot; -exec mysqldump -prepend -t -append analysis_base -append job
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 'SELECT * FROM coord_system'</pre>
<p>
</p>
<hr />
<h1><a name="license">LICENSE</a></h1>
<pre>
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2020] EMBL-European Bioinformatics Institute</pre>
<pre>
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 [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2020] 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</pre>
<pre>
<a href="http://www.apache.org/licenses/LICENSE-2.0">http://www.apache.org/licenses/LICENSE-2.0</a></pre>
<pre>
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.</pre>
<p>
</p>
<hr />
<h1><a name="contact">CONTACT</a></h1>
<pre>
Please subscribe to the Hive mailing list: <a href="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>
<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>
......@@ -4,106 +4,78 @@
<head>
<title>generate_graph.pl</title>
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<link rev="made" href="mailto:_mdnsresponder@scream.apple.com" />
<link rev="made" href="mailto:root@localhost" />
</head>
<body style="background-color: white">
<!-- INDEX BEGIN -->
<div name="index">
<p><a name="__index__"></a></p>
<!--
<ul>
<li><a href="#name">NAME</a></li>
<li><a href="#synopsis">SYNOPSIS</a></li>
<li><a href="#description">DESCRIPTION</a></li>
<li><a href="#options">OPTIONS</a></li>
<li><a href="#external_dependencies">EXTERNAL DEPENDENCIES</a></li>
<li><a href="#license">LICENSE</a></li>
<li><a href="#contact">CONTACT</a></li>
</ul>
-->
</div>
<!-- INDEX END -->
<p>
</p>
<hr />
<h1><a name="name">NAME</a></h1>
<pre>
generate_graph.pl</pre>
<p>
</p>
<hr />
<h1><a name="synopsis">SYNOPSIS</a></h1>
<pre>
./generate_graph.pl [ -url mysql://user:pass@server:port/dbname ] [-pipeconfig TopUp_conf.pm]* -output OUTPUT_LOC [-help]</pre>
<p>
</p>
<hr />
<h1><a name="description">DESCRIPTION</a></h1>
<pre>
This program will generate a graphical representation of your hive pipeline.
<body>
<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 ] [-pipeconfig TopUp_conf.pm]* -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.</pre>
<p>
</p>
<hr />
<h1><a name="options">OPTIONS</a></h1>
<p><strong>--url</strong></p>
<pre>
url defining where hive database is located</pre>
<p><strong>--reg_conf</strong></p>
<pre>
path to a Registry configuration file</pre>
<p><strong>--reg_alias</strong></p>
<pre>
species/alias name for the Hive DBAdaptor</pre>
<p><strong>--pipeconfig</strong></p>
<pre>
A pipeline configuration file that can function both as the initial source of pipeline structure or as a top-up config.
This option can now be used multiple times for multiple top-ups.</pre>
<p><strong>--output</strong></p>
<pre>
Location of the file to write to.
The file extension (.png , .jpeg , .dot , .gif , .ps) will define the output format.</pre>
<p>
</p>
<hr />
<h1><a name="external_dependencies">EXTERNAL DEPENDENCIES</a></h1>
<pre>
GraphViz</pre>
<p>
</p>
<hr />
<h1><a name="license">LICENSE</a></h1>
<pre>
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2020] EMBL-European Bioinformatics Institute</pre>
<pre>
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>--pipeconfig</b></p>
<pre><code> A pipeline configuration file that can function both as the initial source of pipeline structure or as a top-up config.
This option can now be used multiple times for multiple top-ups.</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 [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2020] 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</pre>
<pre>
<a href="http://www.apache.org/licenses/LICENSE-2.0">http://www.apache.org/licenses/LICENSE-2.0</a></pre>
<pre>
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.</pre>
<p>
</p>
<hr />
<h1><a name="contact">CONTACT</a></h1>
<pre>
Please subscribe to the Hive mailing list: <a href="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>
<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>
......@@ -4,123 +4,88 @@
<head>
<title>generate_timeline.pl</title>
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<link rev="made" href="mailto:_mdnsresponder@scream.apple.com" />
<link rev="made" href="mailto:root@localhost" />
</head>
<body style="background-color: white">
<body>
<!-- INDEX BEGIN -->
<div name="index">
<p><a name="__index__"></a></p>
<!--
<ul>
<li><a href="#name">NAME</a></li>
<li><a href="#synopsis">SYNOPSIS</a></li>
<li><a href="#description">DESCRIPTION</a></li>
<li><a href="#usage_examples">USAGE EXAMPLES</a></li>
<li><a href="#options">OPTIONS</a></li>
<li><a href="#external_dependencies">EXTERNAL DEPENDENCIES</a></li>
<li><a href="#license">LICENSE</a></li>
<li><a href="#contact">CONTACT</a></li>
</ul>
-->
<h1 id="NAME">NAME</h1>
<p>generate_timeline.pl</p>
</div>
<!-- INDEX END -->
<h1 id="SYNOPSIS">SYNOPSIS</h1>
<p>
</p>
<hr />
<h1><a name="name">NAME</a></h1>
<p>generate_timeline.pl</p>
<p>
</p>
<hr />
<h1><a name="synopsis">SYNOPSIS</a></h1>
<pre>
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;] }
<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 | pending_workers | pending_time]]
[-key [analysis | resource_class]]
[-n_core &lt;int&gt;] [-mem &lt;int&gt;]</pre>
<p>
</p>
<hr />
<h1><a name="description">DESCRIPTION</a></h1>
[-n_core &lt;int&gt;] [-mem &lt;int&gt;]</code></pre>
<h1 id="DESCRIPTION">DESCRIPTION</h1>
<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 &#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.</p>
<p>You can optionally ask the script to generate an image with Gnuplot.</p>