Thursday’s new experience

Installing the UCSC Genome Browser

At first glance, this looks pretty much idiot-proof, unlike a lot of tools there is a detailed instruction guide, so I thought it would be dead simple.

Hurdle 1, echo $MACHTYPE tells me i386-apple-darwin0.9 The instructions assure me that MACHTYPE will be simple and non-hyphenated. Thinking i’m clever, I type $ export MACHTYPE=i386 then run make libs, and it throws a wobbly about the hyphens in i386-apple-darwin0.9. So off to being more sensible, and editing MACHTYPE in ./profile.

Mistake 1, assuming that MYSQLLIBS and MYSQLINC are set…fix that. Mistake 2, assume you have installed mysql in a standard place, and then fix that.

Mild confusion 1, unzipping jksrc.zip does not give ./kent. Ignore this.
make libs works…the next step cd hg
make compile
does not…google time!
First problem here was:

ld: warning in /usr/local/mysql-5.1.49-osx10.5-x86_64/lib/libmysqlclient.a, file is not of required architecture
So I decided to try another version of mysql which gets past that, then I ran into the same problem as this guy. I went for editing common.mk to SSL=0, as it seemed the quickest (though I am not sure about suggestion 2, as I downloaded the files today and it was set to SSL=1).

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