Source Command


The GORSQL command allows you to run arbitrary SQL commands against “the database” (the database here being defined by the content of a file called gor.db.credentials in the config directory). This command is not enabled when running against a gor-server and therefore does not work within the Sequence Miner. It is intended to be used with GORpipe only.

For GORSQL to work properly, the defined query must access a table have Chrom-POS information as first columns.

SQL statements need to be encapsulated between curly brackets, e.g. gorsql {sql_query}.


gorsql {<sql_query>} | ...


gorsql {select Chrom, Pos, Reference, Call from GWAS_Subset WHERE Phenotype = 'Cancer' order by Chrom,Pos} | ...