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Bio::EnsEMBL::Compara::PipeConfig::ImportUcscChainNet_conf Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::PipeConfig::ImportUcscChainNet_conf:

List of all members.


Class Summary

Synopsis

    #1. Update ensembl-hive, ensembl and ensembl-compara CVS repositories before each new release

    #2. You may need to update 'schema_version' in meta table to the current release number in ensembl-hive/sql/tables.sql

    #3. Download the chain and net files from UCSC
        a) Goto the downloads directory:
          http://hgdownload.cse.ucsc.edu/downloads.html
        b) Select the reference species eg human
        c) Get the chain and net files by selecting the relevant Pairwise Alignments 
        Eg To import the human-human self alignments:
        wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/vsSelf/hg19.hg19.all.chain.gz
        wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/vsSelf/hg19.hg19.net.gz
        d) Get the chromInfo file and the mapping file (if necessary):
          Eg human: Select "Annotation database" from the Human Genome page (step (b) above)
          wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz
          wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ctgPos.txt.gz

    #4. Make sure that all default_options are set correctly, especially:
        release
        pipeline_db (-host)
        resource_classes 
        ref_species (if not homo_sapiens)
        
    #5. Run init_pipeline.pl script: eg for human self alignments
        init_pipeline.pl Bio::EnsEMBL::Compara::PipeConfig::ImportUcscChainNet_conf --dbname hsap_hsap_ucsc_test --password \<your_password) -mlss_id 1 --ref_species homo_sapiens --non_ref_species homo_sapiens --chain_file hg19.hg19.all.chain --net_file hg19.hg19.net --ref_chromInfo_file hsap/chromInfo.txt --ref_ucsc_map ctgPos.txt --config_url '' --ucsc_url http://hgdownload.cse.ucsc.edu/goldenPath/hg19/vsSelf/

    #5. Run the "beekeeper.pl ... -loop" command suggested by init_pipeline.pl

Definition at line 38 of file ImportUcscChainNet_conf.pm.

Available Methods

public beekeeper_extra_cmdline_options ()
public db_connect_command ()
public db_execute_command ()
public dbconn_2_mysql ()
public dbconn_2_url ()
public default_options ()
public fully_substituted_string ()
public fully_substituted_structure ()
public hash_leaves ()
public load_cmdline_options ()
public merge_from_rules ()
public new ()
public o ()
public pipeline_analyses ()
public pipeline_create_commands ()
public pipeline_url ()
public pipeline_wide_parameters ()
public pre_options ()
public process_options ()
public resource_classes ()
public root ()
public run ()
public substitute ()
public use_cases ()

Method Documentation

public Bio::EnsEMBL::Compara::PipeConfig::ImportUcscChainNet_conf::default_options ( )

Undocumented method

Code:
click to view

Reimplemented from Bio::EnsEMBL::Compara::PipeConfig::ComparaGeneric_conf.

public Bio::EnsEMBL::Compara::PipeConfig::ImportUcscChainNet_conf::pipeline_analyses ( )

Undocumented method

Code:
click to view

Reimplemented from Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf.

public Bio::EnsEMBL::Compara::PipeConfig::ImportUcscChainNet_conf::pipeline_create_commands ( )

Undocumented method

Code:
click to view

Reimplemented from Bio::EnsEMBL::Compara::PipeConfig::ComparaGeneric_conf.

public Bio::EnsEMBL::Compara::PipeConfig::ImportUcscChainNet_conf::pipeline_wide_parameters ( )

Undocumented method

Code:
click to view

Reimplemented from Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf.

public Bio::EnsEMBL::Compara::PipeConfig::ImportUcscChainNet_conf::resource_classes ( )

Undocumented method

Code:
click to view

Reimplemented from Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf.


The documentation for this class was generated from the following file: