diff --git a/docs/pipelines/fasta.html b/docs/pipelines/fasta.html index 1da17cccfb5702ef81cd7804c26ec0bbd3587f77..1075224d5dcff2c9c39887304c4cf9a133bc16ff 100644 --- a/docs/pipelines/fasta.html +++ b/docs/pipelines/fasta.html @@ -52,21 +52,21 @@ </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><ul><li>ensembl</li><li>ensembl-hive</li><li>bioperl</li></ul><h3 id="PATH">PATH</h3><ul><li>ensembl-hive/scripts</li><li>faToTwoBit (if not using a custom location)</li><li>xdformat (if not using a custom location)</li></ul><h3 id="ENSEMBLCVSROOTDIR">ENSEMBL_CVS_ROOT_DIR</h3><p>Set to the base checkout of Ensembl. We should be able to add <strong>ensembl-hive/sql</strong> onto this path to find the SQL directory for hive e.g.</p><pre><code> export ENSEMBL_CVS_ROOT_DIR=$HOME/work/ensembl-checkouts </code></pre><h3 id="ENSADMINPSW">ENSADMIN_PSW</h3><p>Give the password to use to log into a database server e.g.</p><pre><code> export ENSADMIN_PSW=wibble </code></pre><h2 id="CommandLineArguments">Command Line Arguments</h2><p>Where <strong>Multiple Supported</strong> is supported we allow the user to specify the parameter more than once on the command line. For example species is one of these options e.g. </p><pre><code>-species human -species cele -species yeast@ -</code></pre><table><tr><th>Name </th><th> Type</th><th>Multiple Supported</th><th> Description</th><th>Default</th><th> Required</th></tr><tr><td><code>-registry</code></td><td>String</td><td>No</td><td>Location of the Ensembl registry to use with this pipeline</td><td>-</td><td><strong>YES</strong></td></tr><tr><td><code>-base_path</code></td><td>String</td><td>No</td><td>Location of the dumps</td><td>-</td><td><strong>YES</strong></td></tr><tr><td><code>-pipeline_db -host=</code></td><td>String</td><td>No</td><td>Specify a host for the hive database e.g. <code>-pipeline_db -host=myserver.mysql</code></td><td>See hive generic config</td><td><strong>YES</strong></td></tr><tr><td><code>-pipeline_db -dbname=</code></td><td>String</td><td>No</td><td>Specify a different database to use as the hive DB e.g. <code>-pipeline_db -dbname=my_dumps_test</code></td><td>Uses pipeline name by default</td><td><strong>NO</strong></td></tr><tr><td><code>-ftp_dir</code></td><td>String</td><td>No</td><td>Location of the current FTP directory with the previous release’s files. We will use this to copy DNA files from one release to another. If not given we do not do any reuse</td><td>-</td><td><strong>NO</strong></td></tr><tr><td><code>-species</code></td><td>String</td><td>Yes</td><td>Specify one or more species to process. Pipeline will only <em>consider</em> these species. Use <strong>-force_species</strong> if you want to force a species run</td><td>-</td><td><strong>NO</strong></td></tr><tr><td><code>-force_species</code></td><td>String</td><td>Yes</td><td>Specify one or more species to force through the pipeline. This is useful to force a dump when you know reuse will not do the <em>"right thing"</em></td><td>-</td><td><strong>NO</strong></td></tr><tr><td><code>-dump_types</code></td><td>String</td><td>Yes</td><td>Specify each type of dump you want to produce. Supported values are <strong>dna</strong>, <strong>cdna</strong> and <strong>ncrna</strong></td><td>All</td><td><strong>NO</strong></td></tr><tr><td><code>-db_types</code></td><td>String</td><td>Yes</td><td>The database types to use. Supports the normal db adaptor groups e.g. <strong>core</strong>, <strong>otherfeatures</strong> etc.</td><td>core</td><td><strong>NO</strong></td></tr><tr><td><code>-release</code></td><td>Integer</td><td>No</td><td>The release to dump</td><td>Software version</td><td><strong>NO</strong></td></tr><tr><td><code>-previous_release</code></td><td>Integer</td><td>No</td><td>The previous release to use. Used to calculate reuse</td><td>Software version minus 1</td><td><strong>NO</strong></td></tr><tr><td><code>-blast_servers</code></td><td>String</td><td>Yes</td><td>The servers to copy blast indexes to</td><td>-</td><td><strong>NO</strong></td></tr><tr><td><code>-blast_genomic_dir</code></td><td>String</td><td>No</td><td>Location to copy the DNA blast indexes to</td><td>-</td><td><strong>NO</strong></td></tr><tr><td><code>-blast_genes_dir</code></td><td>String</td><td>No</td><td>Location to copy the DNA gene (cdna, ncrna and protein) indexes to</td><td>-</td><td><strong>NO</strong></td></tr><tr><td><code>-scp_user</code></td><td>String</td><td>No</td><td>User to perform the SCP as. Defaults to the current user</td><td>Current user</td><td><strong>NO</strong></td></tr><tr><td><code>-scp_identity</code></td><td>String</td><td>No</td><td>The SSH identity file to use when performing SCPs. Normally used in conjunction with <strong>-scp_user</strong></td><td>-</td><td><strong>NO</strong></td></tr><tr><td><code>-no_scp</code></td><td>Boolean</td><td>No</td><td>Skip SCP altogether</td><td>0</td><td><strong>NO</strong></td></tr><tr><td><code>-pipeline_name</code></td><td>String</td><td>No</td><td>Name to use for the pipeline</td><td>fasta_dump_$release</td><td><strong>NO</strong></td></tr><tr><td><code>-wublast_exe</code></td><td>String</td><td>No</td><td>Location of the WUBlast indexing binary</td><td>xdformat</td><td><strong>NO</strong></td></tr><tr><td><code>-blat_exe</code></td><td>String</td><td>No</td><td>Location of the Blat indexing binary</td><td>faToTwoBit</td><td><strong>NO</strong></td></tr><tr><td><code>-port_offset</code></td><td>Integer</td><td>No</td><td>The offset of the ports to use when generating blat indexes. This figure is added onto the web database species ID</td><td>30000</td><td><strong>NO</strong></td></tr><tr><td><code>-email</code></td><td>String</td><td>No</td><td>Email to send pipeline summaries to upon its successful completion</td><td>$USER@sanger.ac.uk</td><td><strong>NO</strong></td></tr></table><h2 id="ExampleCommands">Example Commands</h2><h3 id="Toloadusenormally">To load use normally:</h3><pre><code> init_pipeline.pl Bio::EnsEMBL::Pipeline::PipeConfig:FASTA_conf \ +</code></pre><table><tr><th>Name </th><th> Type</th><th>Multiple Supported</th><th> Description</th><th>Default</th><th> Required</th></tr><tr><td><code>-registry</code></td><td>String</td><td>No</td><td>Location of the Ensembl registry to use with this pipeline</td><td>-</td><td><strong>YES</strong></td></tr><tr><td><code>-base_path</code></td><td>String</td><td>No</td><td>Location of the dumps</td><td>-</td><td><strong>YES</strong></td></tr><tr><td><code>-pipeline_db -host=</code></td><td>String</td><td>No</td><td>Specify a host for the hive database e.g. <code>-pipeline_db -host=myserver.mysql</code></td><td>See hive generic config</td><td><strong>YES</strong></td></tr><tr><td><code>-pipeline_db -dbname=</code></td><td>String</td><td>No</td><td>Specify a different database to use as the hive DB e.g. <code>-pipeline_db -dbname=my_dumps_test</code></td><td>Uses pipeline name by default</td><td><strong>NO</strong></td></tr><tr><td><code>-ftp_dir</code></td><td>String</td><td>No</td><td>Location of the current FTP directory with the previous release’s files. We will use this to copy DNA files from one release to another. If not given we do not do any reuse</td><td>-</td><td><strong>NO</strong></td></tr><tr><td><code>-species</code></td><td>String</td><td>Yes</td><td>Specify one or more species to process. Pipeline will only <em>consider</em> these species. Use <strong>-force_species</strong> if you want to force a species run</td><td>-</td><td><strong>NO</strong></td></tr><tr><td><code>-force_species</code></td><td>String</td><td>Yes</td><td>Specify one or more species to force through the pipeline. This is useful to force a dump when you know reuse will not do the <em>"right thing"</em></td><td>-</td><td><strong>NO</strong></td></tr><tr><td><code>-dump_types</code></td><td>String</td><td>Yes</td><td>Specify each type of dump you want to produce. Supported values are <strong>dna</strong>, <strong>cdna</strong> and <strong>ncrna</strong></td><td>All</td><td><strong>NO</strong></td></tr><tr><td><code>-db_types</code></td><td>String</td><td>Yes</td><td>The database types to use. Supports the normal db adaptor groups e.g. <strong>core</strong>, <strong>otherfeatures</strong> etc.</td><td>core</td><td><strong>NO</strong></td></tr><tr><td><code>-release</code></td><td>Integer</td><td>No</td><td>The release to dump</td><td>Software version</td><td><strong>NO</strong></td></tr><tr><td><code>-previous_release</code></td><td>Integer</td><td>No</td><td>The previous release to use. Used to calculate reuse</td><td>Software version minus 1</td><td><strong>NO</strong></td></tr><tr><td><code>-blast_servers</code></td><td>String</td><td>Yes</td><td>The servers to copy blast indexes to</td><td>-</td><td><strong>NO</strong></td></tr><tr><td><code>-blast_genomic_dir</code></td><td>String</td><td>No</td><td>Location to copy the DNA blast indexes to</td><td>-</td><td><strong>NO</strong></td></tr><tr><td><code>-blast_genes_dir</code></td><td>String</td><td>No</td><td>Location to copy the DNA gene (cdna, ncrna and protein) indexes to</td><td>-</td><td><strong>NO</strong></td></tr><tr><td><code>-scp_user</code></td><td>String</td><td>No</td><td>User to perform the SCP as. Defaults to the current user</td><td>Current user</td><td><strong>NO</strong></td></tr><tr><td><code>-scp_identity</code></td><td>String</td><td>No</td><td>The SSH identity file to use when performing SCPs. Normally used in conjunction with <strong>-scp_user</strong></td><td>-</td><td><strong>NO</strong></td></tr><tr><td><code>-no_scp</code></td><td>Boolean</td><td>No</td><td>Skip SCP altogether</td><td>0</td><td><strong>NO</strong></td></tr><tr><td><code>-pipeline_name</code></td><td>String</td><td>No</td><td>Name to use for the pipeline</td><td>fasta_dump_$release</td><td><strong>NO</strong></td></tr><tr><td><code>-wublast_exe</code></td><td>String</td><td>No</td><td>Location of the WUBlast indexing binary</td><td>xdformat</td><td><strong>NO</strong></td></tr><tr><td><code>-blat_exe</code></td><td>String</td><td>No</td><td>Location of the Blat indexing binary</td><td>faToTwoBit</td><td><strong>NO</strong></td></tr><tr><td><code>-port_offset</code></td><td>Integer</td><td>No</td><td>The offset of the ports to use when generating blat indexes. This figure is added onto the web database species ID</td><td>30000</td><td><strong>NO</strong></td></tr><tr><td><code>-email</code></td><td>String</td><td>No</td><td>Email to send pipeline summaries to upon its successful completion</td><td>$USER@sanger.ac.uk</td><td><strong>NO</strong></td></tr></table><h2 id="ExampleCommands">Example Commands</h2><h3 id="Toloadusenormally">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 -registry reg.pm -</code></pre><h3 id="Runasubsetofspeciesnoforcingsupportsregistryaliases">Run a subset of species (no forcing & supports registry aliases):</h3><pre><code> init_pipeline.pl Bio::EnsEMBL::Pipeline::PipeConfig:FASTA_conf \ +</code></pre><h3 id="Runasubsetofspeciesnoforcingsupportsregistryaliases">Run a subset of species (no forcing & 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 -registry reg.pm -</code></pre><h3 id="Specifyingspeciestoforcesupportsallregistryaliases">Specifying species to force (supports all registry aliases):</h3><pre><code> init_pipeline.pl Bio::EnsEMBL::Pipeline::PipeConfig:FASTA_conf \ +</code></pre><h3 id="Specifyingspeciestoforcesupportsallregistryaliases">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 -registry reg.pm -</code></pre><h3 id="Runningforcingaspecies">Running & forcing a species:</h3><pre><code> init_pipeline.pl Bio::EnsEMBL::Pipeline::PipeConfig:FASTA_conf \ +</code></pre><h3 id="Runningforcingaspecies">Running & 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 -registry reg.pm -</code></pre><h3 id="DumpingjustgenedatanoDNAorncRNA">Dumping just gene data (no DNA or ncRNA):</h3><pre><code> init_pipeline.pl Bio::EnsEMBL::Pipeline::PipeConfig:FASTA_conf \ +</code></pre><h3 id="DumpingjustgenedatanoDNAorncRNA">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 -registry reg.pm -</code></pre><h3 id="UsingadifferentSCPuseridentity">Using a different SCP user & identity:</h3><pre><code> init_pipeline.pl Bio::EnsEMBL::Pipeline::PipeConfig:FASTA_conf \ +</code></pre><h3 id="UsingadifferentSCPuseridentity">Using a different SCP user & 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 -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>&1</code> is important as this clobbers STDERR into STDOUT</li><li><code>> 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>&1 > my_run.log &</code></li><li>Wait</li></ol></body></html> \ No newline at end of file diff --git a/docs/pipelines/fasta.textile b/docs/pipelines/fasta.textile index 8999e3fd058f714dc5b8b74b3432f9d99d3b6639..97d6665662bb977d7081c49e687b7468d6868399 100644 --- a/docs/pipelines/fasta.textile +++ b/docs/pipelines/fasta.textile @@ -154,41 +154,41 @@ h2. Example Commands h3. To load use normally: bc. - init_pipeline.pl Bio::EnsEMBL::Pipeline::PipeConfig:FASTA_conf \ + init_pipeline.pl Bio::EnsEMBL::Pipeline::PipeConfig::FASTA_conf \ -pipeline_db -host=my-db-host -base_path /path/to/dumps -registry reg.pm h3. Run a subset of species (no forcing & supports registry aliases): bc. - init_pipeline.pl Bio::EnsEMBL::Pipeline::PipeConfig:FASTA_conf \ + 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 -registry reg.pm h3. Specifying species to force (supports all registry aliases): bc. - init_pipeline.pl Bio::EnsEMBL::Pipeline::PipeConfig:FASTA_conf \ + 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 -registry reg.pm h3. Running & forcing a species: bc. - init_pipeline.pl Bio::EnsEMBL::Pipeline::PipeConfig:FASTA_conf \ + 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 -registry reg.pm h3. Dumping just gene data (no DNA or ncRNA): bc. - init_pipeline.pl Bio::EnsEMBL::Pipeline::PipeConfig:FASTA_conf \ + init_pipeline.pl Bio::EnsEMBL::Pipeline::PipeConfig::FASTA_conf \ -pipeline_db -host=my-db-host -dump_type cdna \ -base_path /path/to/dumps -registry reg.pm h3. Using a different SCP user & identity: bc. - init_pipeline.pl Bio::EnsEMBL::Pipeline::PipeConfig:FASTA_conf \ + 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 -registry reg.pm