GORSQL¶
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}.
Usage¶
gorsql {<sql_query>} | ...
Examples¶
gorsql {select Chrom, Pos, Reference, Call from GWAS_Subset WHERE Phenotype = 'Cancer' order by Chrom,Pos} | ...