galaxy just wraps existing tools... so it's probably not galaxy that is slow
per se, but the fastqgroomer too. Each tool has its own performance
I don't use fastqgroomer, so I don't know how it can be expected to perform.
Are you sure you need it?
If you know that your error is scaled in sanger units (iontorrent and casava
1.8 fastqs are), then you may not.
If you look at your activity monitor you can see if CPU or disk is the limiting
factor for the work you are doing.
On Jul 24, 2012, at 3:41 PM, Di Nguyen wrote:
> Dear All,
> I successfully install Galaxy onto my new MBP with 16Gb or Ram but when I
> tried to use Galaxy, it is painfully slow! The first test I did was to create
> Admin and import data (RNA-seq fastq, about 6Gb in size) into database and
> then history and it worked fine. The second test was to run fasqgroomer on
> this fasq and it took forever (3 hours+).
> Anybody got in idea of why it is so slow? Would it be possible that Galaxy
> was set up to run a single process instead of 8-core processor? If that is
> the case, how to fix it?
> Please help!
> Di Nguyen
> Postdoc, U of W, Seattle, WA
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