[Genome] hgLoadBed and local-infile option

[Hiram Clawson]

Good Morning Ulas:

Good Morning Ulas:

To avoid this problem, use the option -onServer to your hgLoadBed command.
You can see how the LOCAL gets into the command in the source tree
code src/hg/lib/jksql.c sqlLoadTabFile() function.  And in the hgLoadBed
source, src/hg/makeDb/hgLoadBed/hgLoadBed.c
	int loadOptions = (optionExists("onServer") ? SQL_TAB_FILE_ON_SERVER : 0);

--Hiram

Ulas Karaoz wrote:
> Hi,
> My question is about the "hgLoadBed" binary in Kent source tree. My 
> understanding is that this involves "LOAD DATA" and hence requires to 
> turning on local-infile option when running mysql daemon.
> However, even if it is turned ON, it still complains about the "LOAD 
> DATA" query (see below). When I do execute this command manually, it 
> works fine.
> Does anyone know where this binary get its mysql options when running mysql?
> Thanks.
> ulas.
> 
> ----------------------
> Can't start query:
> LOAD DATA  LOCAL INFILE 'bed.tab'  INTO TABLE test
> 
> mySQL error 1148: The used command is not allowed with this MySQL version
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>