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where SHARED is your group shared account that will be given to you and DATABASE is the name of the database. The .my.cnf file is a text file that is created by the | where SHARED is your group shared account that will be given to you and DATABASE is the name of the database. The .my.cnf file is a text file that is created by the administrator and it contains all information that is required to make a MySQL connection from GBrowse. | ||
If you decide to make use postgres you need firs give a read access by the shared account for the database you want to use. This can be done the | If you decide to make use postgres you need firs give a read access by the shared account for the database you want to use. This can be done the administrator only. Please sens a request to support@computecanada.ca | ||
===Upload Files to Database=== | |||
This can be done by using BioPerl module. Here are commands that need to be run. | |||
* module load bioperl/1.7.1 | |||
* bp_seqfeature_load.pl -c –d USERNAME_example_genome:mysql_read_default_file=/home/USERNAME/.my.cnf example_genomic_sequence.fa header_file | |||
where in this example USERNAME is your username, USERNAME_example_genome is name of your database and example_genomic_sequence.fa is the fasta file containing the entire genome that you want to visualize on gbrowse. header_file contains details about the length of the chromosomes. Here is an example of header file: | |||
##sequence-region I 1 15072434 | |||
##sequence-region II 1 15279421 | |||
##sequence-region III 1 13783801 | |||
##sequence-region IV 1 17493829 | |||
##sequence-region V 1 20924180 | |||
##sequence-region X 1 17718942 | |||
##sequence-region MtDNA 1 13794 | |||
Please note that | |||