Commit 171a79ce authored by Matthieu Muffato's avatar Matthieu Muffato
Browse files

docfix: We don't run the base ProteinTrees_conf pipeline directly

parent a68743c6
......@@ -74,7 +74,7 @@
<p>A couple of more complicated examples:
<pre>
<a href=scripts/init_pipeline.html><b>init_pipeline.pl</b></a> Bio::EnsEMBL::Compara::PipeConfig::ProteinTrees_conf -user "my_db_username" -password "my_db_password" -mlss_id 12345
<a href=scripts/init_pipeline.html><b>init_pipeline.pl</b></a> Bio::EnsEMBL::Compara::PipeConfig::Example::EnsemblProteinTrees_conf -user "my_db_username" -password "my_db_password" -mlss_id 12345
</pre>
<p>It sets 'user', 'password' and 'mlss_id' parameters via command line options.
At this stage you can also override any of the other options mentioned in the default_options section of the PipeConfig file.</p>
......@@ -82,7 +82,7 @@
<p>If you need to modify second-level values of a "hash option" (such as the '-host' or '-port' of the 'pipeline_db' option),
the syntax is the following (follows the extended syntax of Getopt::Long) :
<pre>
<a href=scripts/init_pipeline.html><b>init_pipeline.pl</b></a> Bio::EnsEMBL::Compara::PipeConfig::ProteinTrees_conf -pipeline_db -host=myhost -pipeline_db -port=5306
<a href=scripts/init_pipeline.html><b>init_pipeline.pl</b></a> Bio::EnsEMBL::Compara::PipeConfig::Example::EnsemblProteinTrees_conf -pipeline_db -host=myhost -pipeline_db -port=5306
</pre>
<p><font color=red>PLEASE NOTE</font>:
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