Genome Browser Installation question

[Kathelyn Zelaya]

Good Morning :)

I am having trouble installing the genome browser. 

I am working on an ubuntu terminal with LAMP server installed.

I am following these instructions:

http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/product/README.building.source

The step I am having trouble on is,

5.  To continue building the CGI binaries

126         $ cd kent/src/hg

127         $ make compile

Once I run the 'make compile' command, I get an error saying:

I checked to see if this path exsists: /usr/local/apache/cgi-bin, and it doesnt.

Again, I am using Ubuntu Server 16.4.02 and have Apache2.

Any help will be really appreciated :)

Thanks :)

Kathelyn Zelaya

[Christopher Lee]

Hi Kathelyn,

Thank you for your question about compiling the Genome Browser source code. Is there a particular reason you need to compile from source rather than simply download our pre-compiled binaries? If you don't need the source itself you can take a look at our Genome Browser in the Cloud (GBiC) setup script which will download these binaries and set up a Genome Browser mirror for you. The script is available from our Genome Store (https://genome-store.ucsc.edu/) and is free for non-commercial use by non-profit organizations, academic institutions, and personal use.

That said, if you do need to compile the source code directly, you need to make sure your Apache setup matches what our makefiles expect. In our case, we use /usr/local/apache/ as our apache root, and so our makefile targets all expect that location to exist. Since you are likely working with a default Apache installation (probably somewhere like /var/www/), you will need to create the directory /usr/local/apache/ and then create symlinks to /var/www/. Step 5 in the documentation you linked explains this process a little further:
http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/product/README.building.source

You may also be interested in the following mirror documentation pages, which explain the pros and cons of different kinds of mirror setups, as well as the steps for a manual installation:
http://genome.ucsc.edu/goldenPath/help/mirror.html
http://genome.ucsc.edu/goldenPath/help/mirrorManual.html

Please let us know if you have any further questions!

Thank you again for your inquiry and using the UCSC Genome Browser. If
you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a
publicly-accessible forum. If your question includes sensitive data,
you may send it instead to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute

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