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Commit 21f28aee authored by Matthieu Muffato's avatar Matthieu Muffato
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Regenerated the scripts documentation using a recent toolchain

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docs/scripts/beekeeper.html
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<head>
<title>beekeeper.pl</title>
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<link rev="made" href="mailto:vxd@glow.apple.com" />
<link rev="made" href="mailto:root@localhost" />
</head>
<body style="background-color: white">
<body>
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<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
......@@ -99,13 +99,13 @@
-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&#39;ed ones back to READY so they can be rerun
-reset_all_jobs : reset ALL jobs of -analyses_filter&#39;ed ones back to READY so they can be rerun</code></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
<pre><code> Copyright [2016-2020] 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
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docs/scripts/create_sql_patches.html
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<head>
<title>create_sql_patches.pl</title>
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<link rev="made" href="mailto:vxd@glow.apple.com" />
<link rev="made" href="mailto:root@localhost" />
</head>
<body style="background-color: white">
<body>
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docs/scripts/db_cmd.html
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<head>
<title>db_cmd.pl</title>
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<link rev="made" href="mailto:vxd@glow.apple.com" />
<link rev="made" href="mailto:root@localhost" />
</head>
<body style="background-color: white">
<body>
......@@ -39,7 +39,7 @@
<h1 id="LICENSE">LICENSE</h1>
<pre><code> Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
<pre><code> Copyright [2016-2020] 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
......
docs/scripts/generate_graph.html
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<head>
<title>generate_graph.pl</title>
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<link rev="made" href="mailto:vxd@glow.apple.com" />
<link rev="made" href="mailto:root@localhost" />
</head>
<body style="background-color: white">
<body>
......@@ -58,7 +58,7 @@
<h1 id="LICENSE">LICENSE</h1>
<pre><code> Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
<pre><code> Copyright [2016-2020] 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
......
docs/scripts/generate_timeline.html
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<head>
<title>generate_timeline.pl</title>
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<link rev="made" href="mailto:vxd@glow.apple.com" />
<link rev="made" href="mailto:root@localhost" />
</head>
<body style="background-color: white">
<body>
......@@ -71,8 +71,7 @@
<h1 id="LICENSE">LICENSE</h1>
<p>Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
<p>Copyright [2016-2020] EMBL-European Bioinformatics Institute</p>
<p>Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2020] EMBL-European Bioinformatics Institute</p>
<p>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</p>
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docs/scripts/hoover_pipeline.html
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<head>
<title>hoover_pipeline.pl</title>
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<link rev="made" href="mailto:vxd@glow.apple.com" />
<link rev="made" href="mailto:root@localhost" />
</head>
<body style="background-color: white">
<body>
......@@ -39,10 +39,21 @@
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="OPTIONS">OPTIONS</h1>
<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
-nosqlvc &lt;0|1&gt; : skip sql version check if 1
-before_datetime &lt;string&gt; : delete jobs &#39;DONE&#39; before a specific time
-days_ago &lt;num&gt; : delete jobs that have been &#39;DONE&#39; for at least &lt;num&gt; days
-h | -help : show this help message</code></pre>
<h1 id="LICENSE">LICENSE</h1>
<pre><code> Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
<pre><code> Copyright [2016-2020] 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
......
docs/scripts/init_pipeline.html
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<head>
<title>init_pipeline.pl</title>
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<link rev="made" href="mailto:vxd@glow.apple.com" />
<link rev="made" href="mailto:root@localhost" />
</head>
<body style="background-color: white">
<body>
......@@ -42,7 +42,7 @@
<h1 id="LICENSE">LICENSE</h1>
<pre><code> Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
<pre><code> Copyright [2016-2020] 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
......
docs/scripts/load_resource_usage.html
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<head>
<title>load_resource_usage.pl</title>
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<link rev="made" href="mailto:vxd@glow.apple.com" />
<link rev="made" href="mailto:root@localhost" />
</head>
<body style="background-color: white">
<body>
......@@ -52,7 +52,7 @@
<h1 id="LICENSE">LICENSE</h1>
<pre><code> Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
<pre><code> Copyright [2016-2020] 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
......
docs/scripts/make_docs.html
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<head>
<title>make_docs.pl</title>
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<link rev="made" href="mailto:vxd@glow.apple.com" />
<link rev="made" href="mailto:root@localhost" />
</head>
<body style="background-color: white">
<body>
......@@ -24,7 +24,7 @@
<h1 id="LICENSE">LICENSE</h1>
<pre><code> Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
<pre><code> Copyright [2016-2020] 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
......
docs/scripts/runWorker.html
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<head>
<title>runWorker.pl</title>
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<link rev="made" href="mailto:vxd@glow.apple.com" />
<link rev="made" href="mailto:root@localhost" />
</head>
<body style="background-color: white">
<body>
......@@ -77,7 +77,7 @@
<h1 id="LICENSE">LICENSE</h1>
<pre><code> Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
<pre><code> Copyright [2016-2020] 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
......
docs/scripts/seed_pipeline.html
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<head>
<title>seed_pipeline.pl</title>
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<link rev="made" href="mailto:vxd@glow.apple.com" />
<link rev="made" href="mailto:root@localhost" />
</head>
<body style="background-color: white">
<body>
......@@ -38,7 +38,7 @@
<h1 id="LICENSE">LICENSE</h1>
<pre><code> Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
<pre><code> Copyright [2016-2020] 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
......
docs/scripts/standaloneJob.html
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<head>
<title>standaloneJob.pl</title>
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<link rev="made" href="mailto:vxd@glow.apple.com" />
<link rev="made" href="mailto:root@localhost" />
</head>
<body style="background-color: white">
<body>
......@@ -74,7 +74,7 @@
<h1 id="LICENSE">LICENSE</h1>
<pre><code> Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
<pre><code> Copyright [2016-2020] 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
......
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