Commit 3163615b authored by Andy Yates's avatar Andy Yates
Browse files

Forgot about the registry option given to the command line

parent 737a041c
......@@ -80,6 +80,8 @@ Bio::EnsEMBL::Registry->no_cache_warnings(1);
1;
</code></pre>
<p>You give the registry to the <strong>init_pipeline.pl</strong> script via the <strong>-registry</strong> option</p>
<h2 id="overriding_defaults_using_a_new_config_file">Overriding Defaults Using a New Config File</h2>
<p>We recommend if you have a number of parameters which do not change
......@@ -102,6 +104,8 @@ sub default_options {
1;
</code></pre>
<p>If you do override the config then you should use the package name for your overridden config in the upcoming example commands.</p>
<h2 id="environment">Environment</h2>
<h3 id="perl5lib">PERL5LIB</h3>
......@@ -125,42 +129,42 @@ sub default_options {
<h3 id="to_load_use_normally">To load use normally:</h3>
<pre><code>init_pipeline.pl Bio::EnsEMBL::Pipeline::PipeConfig:FASTA_conf \
-pipeline_db -host=my-db-host -base_path /path/to/dumps
-pipeline_db -host=my-db-host -base_path /path/to/dumps -registry reg.pm
</code></pre>
<h3 id="run_a_subset_of_species_no_forcing_supports_registry_aliases">Run a subset of species (no forcing &amp; supports registry aliases):</h3>
<pre><code>init_pipeline.pl Bio::EnsEMBL::Pipeline::PipeConfig:FASTA_conf \
-pipeline_db -host=my-db-host -species anolis -species celegans -species human \
-base_path /path/to/dumps
-base_path /path/to/dumps -registry reg.pm
</code></pre>
<h3 id="specifying_species_to_force_supports_all_registry_aliases">Specifying species to force (supports all registry aliases):</h3>
<pre><code>init_pipeline.pl Bio::EnsEMBL::Pipeline::PipeConfig:FASTA_conf \
-pipeline_db -host=my-db-host -force_species anolis -force_species celegans -force_species human \
-base_path /path/to/dumps
-base_path /path/to/dumps -registry reg.pm
</code></pre>
<h3 id="running_forcing_a_species">Running &amp; forcing a species:</h3>
<pre><code>init_pipeline.pl Bio::EnsEMBL::Pipeline::PipeConfig:FASTA_conf \
-pipeline_db -host=my-db-host -species celegans -force_species celegans \
-base_path /path/to/dumps
-base_path /path/to/dumps -registry reg.pm
</code></pre>
<h3 id="dumping_just_gene_data">Dumping just gene data:</h3>
<h3 id="dumping_just_gene_data_no_dna_or_ncrna">Dumping just gene data (no DNA or ncRNA):</h3>
<pre><code>init_pipeline.pl Bio::EnsEMBL::Pipeline::PipeConfig:FASTA_conf \
-pipeline_db -host=my-db-host -dump_type cdna \
-base_path /path/to/dumps
-base_path /path/to/dumps -registry reg.pm
</code></pre>
<h3 id="using_a_different_scp_user_identity">Using a different SCP user &amp; identity:</h3>
<pre><code>init_pipeline.pl Bio::EnsEMBL::Pipeline::PipeConfig:FASTA_conf \
-pipeline_db -host=my-db-host -scp_user anotherusr -scp_identity /users/anotherusr/.pri/identity \
-base_path /path/to/dumps
-base_path /path/to/dumps -registry reg.pm
</code></pre>
<h2 id="running_the_pipeline">Running the Pipeline</h2>
......
......@@ -73,6 +73,8 @@ change to version here must be reflected in the configuration file.
1;
You give the registry to the **init_pipeline.pl** script via the **-registry** option
## Overriding Defaults Using a New Config File
We recommend if you have a number of parameters which do not change
......@@ -94,6 +96,8 @@ root config file e.g.
1;
If you do override the config then you should use the package name for your overridden config in the upcoming example commands.
## Environment
### PERL5LIB
......@@ -113,38 +117,37 @@ root config file e.g.
### To load use normally:
init_pipeline.pl Bio::EnsEMBL::Pipeline::PipeConfig:FASTA_conf \
-pipeline_db -host=my-db-host -base_path /path/to/dumps
-pipeline_db -host=my-db-host -base_path /path/to/dumps -registry reg.pm
### Run a subset of species (no forcing & supports registry aliases):
init_pipeline.pl Bio::EnsEMBL::Pipeline::PipeConfig:FASTA_conf \
-pipeline_db -host=my-db-host -species anolis -species celegans -species human \
-base_path /path/to/dumps
-base_path /path/to/dumps -registry reg.pm
### Specifying species to force (supports all registry aliases):
init_pipeline.pl Bio::EnsEMBL::Pipeline::PipeConfig:FASTA_conf \
-pipeline_db -host=my-db-host -force_species anolis -force_species celegans -force_species human \
-base_path /path/to/dumps
-base_path /path/to/dumps -registry reg.pm
### Running & forcing a species:
init_pipeline.pl Bio::EnsEMBL::Pipeline::PipeConfig:FASTA_conf \
-pipeline_db -host=my-db-host -species celegans -force_species celegans \
-base_path /path/to/dumps
-base_path /path/to/dumps -registry reg.pm
### Dumping just gene data:
### Dumping just gene data (no DNA or ncRNA):
init_pipeline.pl Bio::EnsEMBL::Pipeline::PipeConfig:FASTA_conf \
-pipeline_db -host=my-db-host -dump_type cdna \
-base_path /path/to/dumps
-base_path /path/to/dumps -registry reg.pm
### Using a different SCP user & identity:
init_pipeline.pl Bio::EnsEMBL::Pipeline::PipeConfig:FASTA_conf \
-pipeline_db -host=my-db-host -scp_user anotherusr -scp_identity /users/anotherusr/.pri/identity \
-base_path /path/to/dumps
-base_path /path/to/dumps -registry reg.pm
## Running the Pipeline
......
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