Some more docs

docs/pipelines/flatfile.html

@@ -43,4 +43,8 @@
 </code></pre><h3 id="DumpingjustEMBLdatanogenbank">Dumping just EMBL data (no genbank):</h3><pre><code>	init_pipeline.pl Bio::EnsEMBL::Pipeline::PipeConfig::Flatfile_conf \
 	-pipeline_db -host=my-db-host -type embl \
 	-base_path /path/to/dumps -registry reg.pm
-</code></pre><h2 id="RunningthePipeline">Running the Pipeline</h2><ol><li>Start a screen session or get ready to run the beekeeper with a <code>nohup</code></li><li>Choose a dump location<ul><li>A fasta, blast and blat directory will be created 1 level below</li></ul></li><li>Use an <code>init_pipeline.pl</code> configuration from above<ul><li>Make sure to give it the <code>-base_path</code> parameter</li></ul></li><li>Sync the database using one of the displayed from <code>init_pipeline.pl</code></li><li>Run the pipeline in a loop with a good sleep between submissions and redirect log output (the following assumes you are using <strong>bash</strong>)<ul><li><code>2&gt;&amp;1</code> is important as this clobbers STDERR into STDOUT</li><li><code>&gt; my_run.log</code> then sends the output to this file. Use <code>tail -f</code> to track the pipeline</li></ul></li><li><code>beekeeper.pl -url mysql://usr:pass@server:port/db -reg_conf reg.pm -loop -sleep 5 2&gt;&amp;1 &gt; my_run.log &amp;</code></li><li>Wait</li></ol></body></html>
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+</code></pre><h2 id="RunningthePipeline">Running the Pipeline</h2><ol><li>Start a screen session or get ready to run the beekeeper with a <code>nohup</code></li><li>Choose a dump location<ul><li>A fasta, blast and blat directory will be created 1 level below</li></ul></li><li>Use an <code>init_pipeline.pl</code> configuration from above<ul><li>Make sure to give it the <code>-base_path</code> parameter</li></ul></li><li>Sync the database using one of the displayed from <code>init_pipeline.pl</code></li><li>Run the pipeline in a loop with a good sleep between submissions and redirect log output (the following assumes you are using <strong>bash</strong>)<ul><li><code>2&gt;&amp;1</code> is important as this clobbers STDERR into STDOUT</li><li><code>&gt; my_run.log</code> then sends the output to this file. Use <code>tail -f</code> to track the pipeline</li></ul></li><li><code>beekeeper.pl -url mysql://usr:pass@server:port/db -reg_conf reg.pm -loop -sleep 5 2&gt;&amp;1 &gt; my_run.log &amp;</code></li><li>Wait</li></ol><h2 id="RunningwithoutaPipeline">Running without a Pipeline</h2><p>Hive gives us the ability to run any Process outside of a database pipeline <br/>run using <code>standaloneJob.pl</code>. We will list some useful commands to run</p><h3 id="DumpingaSingleSpecies">Dumping a Single Species</h3><pre><code>  standaloneJob.pl Bio::EnsEMBL::Pipeline::FASTA::DumpFile \
+  -reg_conf reg.pm -debug 2 \
+  -release 67 -species homo_sapiens \
+  -base_path /path/to/dumps
+</code></pre></body></html>
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docs/pipelines/flatfile.textile

@@ -135,3 +135,16 @@ h2. Running the Pipeline
 #	@beekeeper.pl -url mysql://usr:pass@server:port/db -reg_conf reg.pm -loop -sleep 5 2>&1 > my_run.log &@
 # Wait
 
+h2. Running without a Pipeline
+
+Hive gives us the ability to run any Process outside of a database pipeline 
+run using @standaloneJob.pl@. We will list some useful commands to run
+
+h3. Dumping a Single Species
+
+bc. 
+  standaloneJob.pl Bio::EnsEMBL::Pipeline::FASTA::DumpFile \
+  -reg_conf reg.pm -debug 2 \
+  -release 67 -species homo_sapiens \
+  -base_path /path/to/dumps
+