Commit 95e5604e authored by Leo Gordon's avatar Leo Gordon
Browse files

bugfix: made sure the non-code references to Examples are also pointing at the new location

parent 62ad8b23
......@@ -18,13 +18,13 @@
4.2 The pipeline is defined in 4 files:
* ensembl-hive/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/DigitFactory.pm splits a multiplication job into sub-tasks and creates corresponding jobs
* ensembl-hive/modules/Bio/EnsEMBL/Hive/Examples/LongMult/RunnableDB/DigitFactory.pm splits a multiplication job into sub-tasks and creates corresponding jobs
* ensembl-hive/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/PartMultiply.pm performs a partial multiplication and stores the intermediate result in a table
* ensembl-hive/modules/Bio/EnsEMBL/Hive/Examples/LongMult/RunnableDB/PartMultiply.pm performs a partial multiplication and stores the intermediate result in a table
* ensembl-hive/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/AddTogether.pm waits for partial multiplication results to compute and adds them together into final result
* ensembl-hive/modules/Bio/EnsEMBL/Hive/Examples/LongMult/RunnableDB/AddTogether.pm waits for partial multiplication results to compute and adds them together into final result
* ensembl-hive/modules/Bio/EnsEMBL/Hive/PipeConfig/LongMult_conf.pm the pipeline configuration module that links the previous Runnables into one pipeline
* ensembl-hive/modules/Bio/EnsEMBL/Hive/Examples/LongMult/PipeConfig/LongMult_conf.pm the pipeline configuration module that links the previous Runnables into one pipeline
4.3 The main part of any PipeConfig file, pipeline_analyses() method, defines the pipeline graph whose nodes are analyses and whose arcs are control and dataflow rules.
Each analysis hash must have:
......@@ -45,7 +45,7 @@
Have another look at LongMult_conf.pm file. The default_options() method returns a hash that pretty much defines what parameters you can/should supply to init_pipeline.pl .
You will probably need to specify the following:
$ init_pipeline.pl Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf \
$ init_pipeline.pl Bio::EnsEMBL::Hive::Examples::LongMult::PipeConfig::LongMult_conf \
-host=<your_mysql_host> \
-port=<your_mysql_port> \
-user=<your_mysql_username> \
......
......@@ -58,7 +58,7 @@
This is done by feeding the PipeConfig file to ensembl-hive/scripts/<a href=scripts/init_pipeline.html><b>init_pipeline.pl</b></a> script.<br/>
A typical example:
<pre>
<a href=scripts/init_pipeline.html><b>init_pipeline.pl</b></a> Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf -pipeline_url mysql://user:password@host:port/long_mult
<a href=scripts/init_pipeline.html><b>init_pipeline.pl</b></a> Bio::EnsEMBL::Hive::Examples::LongMult::PipeConfig::LongMult_conf -pipeline_url mysql://user:password@host:port/long_mult
</pre>
<p>It will create a MySQL pipeline database called 'long_mult' with the given connection parameters.
......@@ -66,7 +66,7 @@
<p>If heavy concurrent traffic to the database is not expected, we may choose to keep the blackboard in a local SQLite file:
<pre>
<a href=scripts/init_pipeline.html><b>init_pipeline.pl</b></a> Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf -pipeline_url sqlite:///long_mult
<a href=scripts/init_pipeline.html><b>init_pipeline.pl</b></a> Bio::EnsEMBL::Hive::Examples::LongMult::PipeConfig::LongMult_conf -pipeline_url sqlite:///long_mult
</pre>
<p>
In the latter case no other connection parameters except for the filename are necessary, so they are skipped.
......@@ -169,7 +169,7 @@
<p>Actually, you don't even need to generate a pipeline database to see its diagram,
as the diagram can be generated directly from the PipeConfig file:
<pre>
<a href=scripts/generate_graph.html><b>generate_graph.pl</b></a> -pipeconfig Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf -out my_diagram2.png
<a href=scripts/generate_graph.html><b>generate_graph.pl</b></a> -pipeconfig Bio::EnsEMBL::Hive::Examples::LongMult::PipeConfig::LongMult_conf -out my_diagram2.png
</pre>
<p>
Such a "standalone" diagram may look slightly different (analysis_ids will be missing).
......
......@@ -57,7 +57,7 @@
-flow_into &quot;{ 1 =&gt; &#39;mysql://ensadmin:xxxxxxx@127.0.0.1/lg4_long_mult/analysis?logic_name=start&#39; }&quot;
# Produce a semaphore group of jobs from a database-less DigitFactory job:
standaloneJob.pl Bio::EnsEMBL::Hive::RunnableDB::LongMult::DigitFactory -input_id &quot;{ &#39;a_multiplier&#39; =&gt; &#39;2222222222&#39;, &#39;b_multiplier&#39; =&gt; &#39;3434343434&#39;}&quot; \
standaloneJob.pl Bio::EnsEMBL::Hive::Examples::LongMult::RunnableDB::DigitFactory -input_id &quot;{ &#39;a_multiplier&#39; =&gt; &#39;2222222222&#39;, &#39;b_multiplier&#39; =&gt; &#39;3434343434&#39;}&quot; \
-flow_into &quot;{ &#39;2-&gt;A&#39; =&gt; &#39;mysql://ensadmin:${ENSADMIN_PSW}@127.0.0.1/lg4_long_mult/analysis?logic_name=part_multiply&#39;, &#39;A-&gt;1&#39; =&gt; &#39;mysql://ensadmin:${ENSADMIN_PSW}@127.0.0.1/lg4_long_mult/analysis?logic_name=add_together&#39; }&quot; </code></pre>
<h1 id="SCRIPT-SPECIFIC-OPTIONS">SCRIPT-SPECIFIC OPTIONS</h1>
......
......@@ -6,7 +6,7 @@
=head1 SYNOPSIS
Please refer to Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf pipeline configuration file
Please refer to Bio::EnsEMBL::Hive::Examples::LongMult::PipeConfig::LongMult_conf pipeline configuration file
to understand how this particular example pipeline is configured and ran.
=head1 DESCRIPTION
......
......@@ -6,7 +6,7 @@
=head1 SYNOPSIS
Please refer to Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf pipeline configuration file
Please refer to Bio::EnsEMBL::Hive::Examples::LongMult::PipeConfig::LongMult_conf pipeline configuration file
to understand how this particular example pipeline is configured and ran.
=head1 DESCRIPTION
......
......@@ -6,7 +6,7 @@
=head1 SYNOPSIS
Please refer to Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf pipeline configuration file
Please refer to Bio::EnsEMBL::Hive::Examples::LongMult::PipeConfig::LongMult_conf pipeline configuration file
to understand how this particular example pipeline is configured and ran.
=head1 DESCRIPTION
......
###########################################################################################################################################
#
# Bio::EnsEMBL::Hive::RunnableDB::LongMult is an example eHive pipeline.
#
#
# Please have a look at the pipeline configuration file
#
# ensembl-hive/modules/Bio/EnsEMBL/Hive/Examples/LongMult/PipeConfig/LongMult_conf.pm
#
# which is used to load the Long Multiplication pipeline either in "analysis control" or "semaphore job control" mode.
#
#
# Create this pipeline using init_pipeline.pl and run it using beekeeper.pl in step-by-step mode (use -run instead of -loop option).
#
###########################################################################################################################################
......@@ -113,7 +113,7 @@ __DATA__
-flow_into "{ 1 => 'mysql://ensadmin:xxxxxxx@127.0.0.1/lg4_long_mult/analysis?logic_name=start' }"
# Produce a semaphore group of jobs from a database-less DigitFactory job:
standaloneJob.pl Bio::EnsEMBL::Hive::RunnableDB::LongMult::DigitFactory -input_id "{ 'a_multiplier' => '2222222222', 'b_multiplier' => '3434343434'}" \
standaloneJob.pl Bio::EnsEMBL::Hive::Examples::LongMult::RunnableDB::DigitFactory -input_id "{ 'a_multiplier' => '2222222222', 'b_multiplier' => '3434343434'}" \
-flow_into "{ '2->A' => 'mysql://ensadmin:${ENSADMIN_PSW}@127.0.0.1/lg4_long_mult/analysis?logic_name=part_multiply', 'A->1' => 'mysql://ensadmin:${ENSADMIN_PSW}@127.0.0.1/lg4_long_mult/analysis?logic_name=add_together' }"
......
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