FASTA Pipeline

This is a re-implementation of an existing pipeline developed originally by core and the webteam. The new version uses eHive, so familiarity with this system is essential, and has been written to use as little memory as possible.

The Registry File

This is the way we retrieve the database connections to work with. The registry file should specify:

• The core (and any other) databases to dump from
• A production database
  • species = multi
  • group = production
  • Used to find which species require new DNA
• A web database
  • species = multi
  • group = web
  • Used to name BLAT index files

Here is an example of a file for v67 of Ensembl. Note the use of the Registry object within a registry file and the scoping of the package. If you omit the -db_version parameter and only use HEAD checkouts of Ensembl then this will automatically select the latest version of the API. Any change to version here must be reflected in the configuration file.

package Reg;

use Bio::EnsEMBL::Registry;
use Bio::EnsEMBL::DBSQL::DBAdaptor;

Bio::EnsEMBL::Registry->no_version_check(1);
Bio::EnsEMBL::Registry->no_cache_warnings(1);

{
  my $version = 67;
  Bio::EnsEMBL::Registry->load_registry_from_multiple_dbs(
    {
      -host => "mydb-1",
      -port => 3306,
      -db_version => $version,
      -user => "user",
      -NO_CACHE => 1,
    },
    {    
      -host => "mydb-2",
      -port => 3306,
      -db_version => $version,
      -user => "user",
      -NO_CACHE => 1,
    },
  );

  Bio::EnsEMBL::DBSQL::DBAdaptor->new(
    -HOST => 'mydb-2',
    -PORT => 3306,
    -USER => 'user',
    -DBNAME => 'ensembl_website',
    -SPECIES => 'multi',
    -GROUP => 'web'
  );

  Bio::EnsEMBL::DBSQL::DBAdaptor->new(
    -HOST => 'mydb-2',
    -PORT => 3306,
    -USER => 'user',
    -DBNAME => 'ensembl_production',
    -SPECIES => 'multi',
    -GROUP => 'production'
  );
}

1;

Overriding Defaults Using a New Config File

We recommend if you have a number of parameters which do not change between releases to create a configuration file which inherits from the root config file e.g.

package MyCnf;

use base qw/Bio::EnsEMBL::Pipeline::FASTA::FASTA_conf/;

sub default_options {
  my ($self) = @_;
  return {
    %{ $self->SUPER::default_options() },

    #Override of options
  };
}

1;

Environment

PERL5LIB

• ensembl
• ensembl-hive
• bioperl

PATH

• ensembl-hive/scripts
• faToTwoBit (if not using a custom location)
• xdformat (if not using a custom location)

Example Commands

To load use normally:

init_pipeline.pl Bio::EnsEMBL::Pipeline::PipeConfig:FASTA_conf \
-pipeline_db -host=my-db-host -base_path /path/to/dumps

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

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

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

Dumping just gene data:

init_pipeline.pl Bio::EnsEMBL::Pipeline::PipeConfig:FASTA_conf \
-pipeline_db -host=my-db-host -dump_type cdna \
-base_path /path/to/dumps

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

Running the Pipeline

1. Start a screen session or get ready to run the beekeeper with a nohup
2. Choose a dump location
   • A fasta, blast and blat directory will be created 1 level below
3. Use an init_pipeline.pl configuration from above
   • Make sure to give it the -base_path parameter
4. Sync the database using one of the displayed from init_pipeline.pl

5. Run the pipeline in a loop with a good sleep between submissions and redirect log output (the following assumes you are using bash)

   • 2>&1 is important as this clobbers STDERR into STDOUT
   • > myrun.log then sends the output to this file. Use tail -f to track the pipeline beekeeper.pl -url mysql://usr:pass@server:port/db -regconf reg.pm -loop -sleep 5 2>&1 > my_run.log &

6. Wait