Ensembl data load

Load Repeatmasker file

• The make things easier, let's set a little shortcut:

export DBSPEC="-dbhost 127.0.0.1 -dbuser ens-training -dbport 3306 -dbname mouse37_mini_ref -dbpass workshop"

• Run repeatmasker on a fasta file:

RepeatMasker -species mouse -qq -dir <full_path_to_output_directory> $HOME/workshop/genebuild/test_seqs/test_sequence_to_repeatmask.fa

• Create a "dummy analysis file" which will simply select the sequences to analyse (here: contigs), e.g. create a file submit_ana.conf:

[SubmitContig]
module=Dummy
input_id_type=CONTIG

• Load the "dummy analysis"

$HOME/cvs_checkout/ensembl-pipeline/scripts/analysis_setup.pl $DBSPEC -read -file repeatmask_ana.conf 

• Define the real analysis, e.g. repeatmask_ana.conf

[RepeatMask]
db=repbase
db_version=0129
db_file=repbase
program=RepeatMask
program_version=3.1.8
program_file=/path/to/repmasker/RepeatMask
parameters=-nolow -species mouse -s
module=RepeatMask
gff_source=RepeatMask
gff_feature=repeat
input_id_type=CONTIG

• load the analysis into the mysql database

$HOME/cvs_checkout/ensembl-pipeline/scripts/analysis_setup.pl $DBSPEC -read -file repeatmask_ana.conf

• see what happened:

SELECT * from analysis\G
*************************** 1. row ***************************
   analysis_id: 1
       created: 2010-09-13 16:50:16
    logic_name: SubmitContig
            db: NULL
    db_version: NULL
       db_file: NULL
       program: NULL
program_version: NULL
  program_file: NULL
    parameters: NULL
        module: Dummy
module_version: NULL
    gff_source: NULL
   gff_feature: NULL

*************************** 2. row ***************************
   analysis_id: 2
       created: 2010-09-13 16:14:11
    logic_name: RepeatMask
            db: repbase
    db_version: 0129
       db_file: repbase
       program: RepeatMask
program_version: 3.1.8
  program_file: /path/to/repmasker/RepeatMask
    parameters: -nolow -species mouse -s
        module: RepeatMask
module_version: NULL
    gff_source: RepeatMask
   gff_feature: repeat