Commit 51a8f0e2 authored by Matthieu Muffato's avatar Matthieu Muffato
Browse files

Regenerated the scripts documentation using a recent toolchain

parent cd98ddb8
...@@ -7,124 +7,80 @@ ...@@ -7,124 +7,80 @@
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<div name="index"> <h1 id="NAME">NAME</h1>
<p><a name="__index__"></a></p>
<!-- <pre><code> beekeeper.pl [options]</code></pre>
<ul> <h1 id="DESCRIPTION">DESCRIPTION</h1>
<li><a href="#name">NAME</a></li> <pre><code> The Beekeeper is in charge of interfacing between the Queen and a compute resource or &#39;compute farm&#39;.
<li><a href="#description">DESCRIPTION</a></li>
<li><a href="#usage_examples">USAGE EXAMPLES</a></li>
<li><a href="#options">OPTIONS</a></li>
<ul>
<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>
<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>
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 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> and to send the requested number of workers to open machines via the runWorker.pl script.
<pre>
It is also responsible for interfacing with the Queen to identify workers which died 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> unexpectedly so that she can free the dead workers and reclaim unfinished jobs.</code></pre>
<p>
</p> <h1 id="USAGE-EXAMPLES">USAGE EXAMPLES</h1>
<hr />
<h1><a name="usage_examples">USAGE EXAMPLES</a></h1> <pre><code> # Usually run after the pipeline has been created to calculate the internal statistics necessary for eHive functioning
<pre> beekeeper.pl -url mysql://username:secret@hostname:port/ehive_dbname -sync
# 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: # 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> beekeeper.pl -url mysql://username:secret@hostname:port/ehive_dbname
<pre>
# 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
beekeeper.pl -url mysql://username:secret@hostname:port/long_mult_test -analyses_pattern 'blast%-4..6' -loop</pre> beekeeper.pl -url mysql://username:secret@hostname:port/long_mult_test -analyses_pattern &#39;blast%-4..6&#39; -loop
<pre>
# Restrict the normal execution to one iteration only - can be used for testing a newly set up pipeline # 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> beekeeper.pl -url mysql://username:secret@hostname:port/long_mult_test -run
<pre>
# Reset failed 'buggy_analysis' jobs to 'READY' state, so that they can be run again # 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</pre> beekeeper.pl -url mysql://username:secret@hostname:port/long_mult_test -analyses_pattern buggy_analysis -reset_failed_jobs
<pre>
# Do a cleanup: find and bury dead workers, reclaim their 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> beekeeper.pl -url mysql://username:secret@hostname:port/long_mult_test -dead</code></pre>
<p>
</p> <h1 id="OPTIONS">OPTIONS</h1>
<hr />
<h1><a name="options">OPTIONS</a></h1> <h2 id="Connection-parameters">Connection parameters</h2>
<p>
</p> <pre><code> -reg_conf &lt;path&gt; : path to a Registry configuration file
<h2><a name="connection_parameters">Connection parameters</a></h2> -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;)
<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')
-reg_alias &lt;string&gt; : species/alias name for the Hive DBAdaptor -reg_alias &lt;string&gt; : species/alias name for the Hive DBAdaptor
-url &lt;url string&gt; : url defining where hive database is located -url &lt;url string&gt; : url defining where hive database is located
-nosqlvc &lt;0|1&gt; : skip sql version check if 1</pre> -nosqlvc &lt;0|1&gt; : skip sql version check if 1</code></pre>
<p>
</p> <h2 id="Configs-overriding">Configs overriding</h2>
<h2><a name="configs_overriding">Configs overriding</a></h2>
<pre> <pre><code> -config_file &lt;string&gt; : json file (with absolute path) to override the default configurations (could be multiple)</code></pre>
-config_file &lt;string&gt; : json file (with absolute path) to override the default configurations (could be multiple)</pre>
<p> <h2 id="Looping-control">Looping control</h2>
</p>
<h2><a name="looping_control">Looping control</a></h2> <pre><code> -loop : run autonomously, loops and sleeps
<pre>
-loop : run autonomously, loops and sleeps
-max_loops &lt;num&gt; : perform max this # of loops in autonomous mode -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 -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 -job_id &lt;job_id&gt; : run 1 iteration for this job_id
-run : run 1 iteration of automation loop -run : run 1 iteration of automation loop
-sleep &lt;num&gt; : when looping, sleep &lt;num&gt; minutes (default 1 min)</pre> -sleep &lt;num&gt; : when looping, sleep &lt;num&gt; minutes (default 1 min)</code></pre>
<p>
</p> <h2 id="Current-Meadow-control">Current Meadow control</h2>
<h2><a name="current_meadow_control">Current Meadow control</a></h2>
<pre> <pre><code> -meadow_type &lt;string&gt; : the desired Meadow class name, such as &#39;LSF&#39; or &#39;LOCAL&#39;
-meadow_type &lt;string&gt; : the desired Meadow class name, such as 'LSF' or 'LOCAL'
-total_running_workers_max &lt;num&gt; : max # workers to be running in parallel -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 -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) -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> -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>
<p>
</p> <h2 id="Worker-control">Worker control</h2>
<h2><a name="worker_control">Worker control</a></h2>
<pre> <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
-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 -can_respecialize &lt;0|1&gt; : 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 &lt;worker_id&gt; : kill worker by worker_id -killworker &lt;worker_id&gt; : kill worker by worker_id
...@@ -132,12 +88,11 @@ ...@@ -132,12 +88,11 @@
-job_limit &lt;num&gt; : #jobs to run before worker can die naturally -job_limit &lt;num&gt; : #jobs to run before worker can die naturally
-retry_throwing_jobs &lt;0|1&gt; : if a job dies *knowingly*, should we retry it by default? -retry_throwing_jobs &lt;0|1&gt; : 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 -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> -debug &lt;debug_level&gt; : set debug level of the workers</code></pre>
<p>
</p> <h2 id="Other-commands-options">Other commands/options</h2>
<h2><a name="other_commands_options">Other commands/options</a></h2>
<pre> <pre><code> -help : print this help
-help : print this help
-versions : report both Hive code version and Hive database schema version -versions : report both Hive code version and Hive database schema version
-dead : detect all unaccounted dead workers and reset their jobs for resubmission -dead : detect all unaccounted dead workers and reset their jobs for resubmission
-sync : re-synchronize the hive -sync : re-synchronize the hive
...@@ -148,31 +103,30 @@ ...@@ -148,31 +103,30 @@
-failed_jobs : show all failed jobs -failed_jobs : show all failed jobs
-job_output &lt;job_id&gt; : print details for one job -job_output &lt;job_id&gt; : print details for one job
-reset_job_id &lt;num&gt; : reset a job back to READY so it can be rerun -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_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_filter'ed ones back to READY so they can be rerun</pre> -reset_all_jobs : reset ALL jobs of analyses matching -analyses_pattern back to READY so they can be rerun</code></pre>
<p>
</p> <h1 id="LICENSE">LICENSE</h1>
<hr />
<h1><a name="license">LICENSE</a></h1> <pre><code> Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
<pre> Copyright [2016-2020] EMBL-European Bioinformatics Institute
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2020] EMBL-European Bioinformatics Institute</pre>
<pre>
Licensed under the Apache License, Version 2.0 (the &quot;License&quot;); you may not use this file except in compliance with the License. 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> You may obtain a copy of the License at
<pre>
<a href="http://www.apache.org/licenses/LICENSE-2.0">http://www.apache.org/licenses/LICENSE-2.0</a></pre> http://www.apache.org/licenses/LICENSE-2.0
<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 &quot;AS IS&quot; BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 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> See the License for the specific language governing permissions and limitations under the License.</code></pre>
<p>
</p> <h1 id="CONTACT">CONTACT</h1>
<hr />
<h1><a name="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: <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>
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<p><a name="__index__"></a></p>
<!--
-->
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<!-- INDEX BEGIN -->
<div name="index"> <h1 id="NAME">NAME</h1>
<p><a name="__index__"></a></p>
<!-- <pre><code> db_cmd.pl</code></pre>
<ul> <h1 id="SYNOPSIS">SYNOPSIS</h1>
<li><a href="#name">NAME</a></li> <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; ] [ -sql &lt;sql_command&gt; ] [ -verbose ] [other arguments to append to the command line]</code></pre>
<li><a href="#synopsis">SYNOPSIS</a></li>
<li><a href="#description">DESCRIPTION</a></li> <h1 id="DESCRIPTION">DESCRIPTION</h1>
<li><a href="#usage_examples">USAGE EXAMPLES</a></li>
<li><a href="#license">LICENSE</a></li> <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.
<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; ] [ -sql &lt;sql_command&gt; ] [ -verbose ] [other arguments to append to the command line]</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. -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&#39;s options and the start of the arguments that have to be passed as-is (see the example below with --html)</code></pre>
<p>
</p> <h1 id="USAGE-EXAMPLES">USAGE EXAMPLES</h1>
<hr />
<h1><a name="usage_examples">USAGE EXAMPLES</a></h1> <pre><code> db_cmd.pl -url &quot;mysql://ensadmin:${ENSADMIN_PSW}@localhost:3306/&quot; -sql &#39;CREATE DATABASE lg4_long_mult&#39;
<pre>
db_cmd.pl -url &quot;mysql://ensadmin:${ENSADMIN_PSW}@localhost:3306/&quot; -sql 'CREATE DATABASE lg4_long_mult'
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;
db_cmd.pl -url &quot;mysql://ensadmin:${ENSADMIN_PSW}@localhost:3306/lg4_long_mult&quot; -sql 'SELECT * FROM analysis_base' -- --html db_cmd.pl -url &quot;mysql://ensadmin:${ENSADMIN_PSW}@localhost:3306/lg4_long_mult&quot; -sql &#39;SELECT * FROM analysis_base&#39; -- --html
db_cmd.pl -url &quot;mysql://ensadmin:${ENSADMIN_PSW}@localhost/lg4_long_mult&quot; -exec mysqldump -prepend -t analysis_base job</pre> db_cmd.pl -url &quot;mysql://ensadmin:${ENSADMIN_PSW}@localhost/lg4_long_mult&quot; -exec mysqldump -prepend -t analysis_base job
<pre>
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 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 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> 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>
<p>
</p> <h1 id="LICENSE">LICENSE</h1>
<hr />
<h1><a name="license">LICENSE</a></h1> <pre><code> Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
<pre> Copyright [2016-2020] EMBL-European Bioinformatics Institute
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2020] EMBL-European Bioinformatics Institute</pre>
<pre>
Licensed under the Apache License, Version 2.0 (the &quot;License&quot;); you may not use this file except in compliance with the License. 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> You may obtain a copy of the License at
<pre>
<a href="http://www.apache.org/licenses/LICENSE-2.0">http://www.apache.org/licenses/LICENSE-2.0</a></pre> http://www.apache.org/licenses/LICENSE-2.0
<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 &quot;AS IS&quot; BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 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> See the License for the specific language governing permissions and limitations under the License.</code></pre>
<p>
</p> <h1 id="CONTACT">CONTACT</h1>
<hr />
<h1><a name="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: <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>
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<!-- INDEX BEGIN -->
<div name="index"> <h1 id="NAME">NAME</h1>
<p><a name="__index__"></a></p>
<!-- <pre><code> generate_graph.pl</code></pre>
<ul> <h1 id="SYNOPSIS">SYNOPSIS</h1>
<li><a href="#name">NAME</a></li> <pre><code> ./generate_graph.pl -help
<li><a href="#synopsis">SYNOPSIS</a></li>
<li><a href="#description">DESCRIPTION</a></li> ./generate_graph.pl [ -url mysql://user:pass@server:port/dbname | -reg_conf &lt;reg_conf_file&gt; -reg_alias &lt;reg_alias&gt; ] [-pipeconfig TopUp_conf.pm]* -output OUTPUT_LOC</code></pre>
<li><a href="#options">OPTIONS</a></li>
<li><a href="#external_dependencies">EXTERNAL DEPENDENCIES</a></li> <h1 id="DESCRIPTION">DESCRIPTION</h1>
<li><a href="#license">LICENSE</a></li>
<li><a href="#contact">CONTACT</a></li> <pre><code> This program will generate a graphical representation of your hive pipeline.
</ul>
-->
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<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 -help</pre>
<pre>
./generate_graph.pl [ -url mysql://user:pass@server:port/dbname | -reg_conf &lt;reg_conf_file&gt; -reg_alias &lt;reg_alias&gt; ] [-pipeconfig TopUp_conf.pm]* -output OUTPUT_LOC</pre>
<p>
</p>
<hr />
<h1><a name="description">DESCRIPTION</a></h1>
<pre>
This program will generate a graphical representation of your hive pipeline.
This includes visualising the flow of data from the different analyses, blocking This includes visualising the flow of data from the different analyses, blocking
rules &amp; table writers. The graph is also coloured to indicate the stage 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 an analysis is at. The colours &amp; fonts used can be configured via
hive_config.json configuration file.</pre> hive_config.json configuration file.</code></pre>
<p>
</p> <h1 id="OPTIONS">OPTIONS</h1>
<hr />
<h1><a name="options">OPTIONS</a></h1> <p><b>--url</b></p>
<p><strong>--url</strong></p>
<pre> <pre><code> url defining where hive database is located</code></pre>
url defining where hive database is located</pre>
<p><strong>--reg_conf</strong></p> <p><b>--reg_conf</b></p>
<pre>
path to a Registry configuration file</pre> <pre><code> path to a Registry configuration file</code></pre>
<p><strong>--reg_alias</strong></p>
<pre> <p><b>--reg_alias</b></p>
species/alias name for the Hive DBAdaptor</pre>
<p><strong>--nosqlvc</strong></p> <pre><code> species/alias name for the Hive DBAdaptor</code></pre>
<pre>
if 1, don't check sql schema version</pre> <p><b>--nosqlvc</b></p>
<p><strong>--config_file</strong></p>
<pre> <pre><code> if 1, don&#39;t check sql schema version</code></pre>
Path to JSON hive config file</pre>
<p><strong>--pipeconfig</strong></p> <p><b>--config_file</b></p>
<pre>
A pipeline configuration file that can function both as the initial source of pipeline structure or as a top-up config. <pre><code> Path to JSON hive config file</code></pre>
This option can now be used multiple times for multiple top-ups.</pre>
<p><strong>--format</strong></p> <p><b>--pipeconfig</b></p>
<pre>
(Optional) specify the output format, or override the output format specified by the output file's extension <pre><code> A pipeline configuration file that can function both as the initial source of pipeline structure or as a top-up config.
(e.g. png, jpeg, dot, gif, ps)</pre> This option can now be used multiple times for multiple top-ups.</code></pre>
<p><strong>--output</strong></p>
<pre> <p><b>--format</b></p>
Location of the file to write to.
The file extension (.png , .jpeg , .dot , .gif , .ps) will define the output format.</pre> <pre><code> (Optional) specify the output format, or override the output format specified by the output file&#39;s extension
<p><strong>--help</strong></p> (e.g. png, jpeg, dot, gif, ps)</code></pre>
<pre>
Print this help message</pre> <p><b>--output</b></p>
<p>
</p> <pre><code> Location of the file to write to.
<hr /> The file extension (.png , .jpeg , .dot , .gif , .ps) will define the output format.</code></pre>
<h1><a name="external_dependencies">EXTERNAL DEPENDENCIES</a></h1>
<pre> <p><b>--help</b></p>
GraphViz</pre>
<p> <pre><code> Print this help message</code></pre>
</p>
<hr /> <h1 id="EXTERNAL-DEPENDENCIES">EXTERNAL DEPENDENCIES</h1>
<h1><a name="license">LICENSE</a></h1>
<pre> <pre><code> GraphViz</code></pre>
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2020] EMBL-European Bioinformatics Institute</pre> <h1 id="LICENSE">LICENSE</h1>
<pre>
<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. 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> You may obtain a copy of the License at
<pre>
<a href="http://www.apache.org/licenses/LICENSE-2.0">http://www.apache.org/licenses/LICENSE-2.0</a></pre> http://www.apache.org/licenses/LICENSE-2.0
<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 &quot;AS IS&quot; BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 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> See the License for the specific language governing permissions and limitations under the License.</code></pre>
<p>
</p> <h1 id="CONTACT">CONTACT</h1>
<hr />
<h1><a name="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: <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>
</body> </body>