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Bioinformatics, Perl, Cool Stuff
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more user specific database work

Lots of work in the last week:

  • loading tair cDNA and EST data (though it is problematic) (2 hours)
  • Installed and configured GBrowse2 (1 hour)
  • Worked on the outline of the rest of the work needed from my side for creating user spaces (5 hours so far)
    • create new db
      • what about organism?

        INSERT INTO organism (abbreviation,genus,species,common_name) VALUES ('T.testus','Test','testus','test');

      • do we want to have analysis entries pre set up?
    • create new gmod conf file?

      cp chado.conf new_name.conf
      perl -pi -e 's/DBNAME=chado/DBNAME=new_name/' new_name.conf
      perl -pi -e 's/DBORGANISM=/DBORGANISM=test/' new_name.conf

    • load given data into new database -a --noexon --dbprof test_db -g test.gff3

    • create a conf file for the data

      put in a link for some region of the input sequence

    • add to gbrowse2.conf

      description = test_db's data
      path = test_db.conf