Genome Browser Sprint this weekend

[Lachlan Musicman]

Hi,

As someone that has struggled with installing GB locally (got there, just before the money ran out), I have nominated what I consider to be a GB issue for this weekend's HealthHack in Australia.

http://healthhack.com.au/ (see Challenge #1 http://healthhack.com.au/currentchallenges.html )

Ideally we will end up with a simplified upload process for GB that we can give back to the community. Minimally, we would like something that works "for us".

When I was installing the GB software this list was very helpful and I was hoping someone at UCSC would be available to keep an eye on the list over this weekend to answer any questions that arise.

I will be available to the teams over the weekend, but GB is a big sprawling software package that I still struggle with - I'd appreciate any help I could get.

cheers

L.

------
The most dangerous phrase in the language is, "We've always done it this way."

- Grace Hopper

[Hiram Clawson]

Good Evening Lachlan:

Your target user base might have a much better time using
the 'browser in a box' already installed in a virtual machine
to be run in Virtual Box:
https://genome-store.ucsc.edu/

So many browser users have attempted to write the 'one script installs
all the genome browser' that it is confusing when you search for
such a script because so many leads go to scripts that are not appropriate
for the particular use case, or they are hopelessly out of date.

Here is a script written by one of our researchers:
https://github.com/maximilianh/browserInstall
which will install everything you need on several different types
of operating systems. It assumes you don't have Apache or MySQL
installed, so it will do that for you, as will as other obscure
fixups to your running operating system. You would not run this
on a system which already has something installed that works with
Apache or MySQL.

--Hiram

[Hiram Clawson]

Highly recommend track hubs, or assembly hubs, which will then work
in any genome browser anywhere and the user is in full control of
their data at all times. i.e. doesn't get lost from a genome browser
instance. This does require the hurdle of having
access to a directory that can be served up by Apache from the
institution of the user. This is often a show stopper.

On 10/22/15 6:30 PM, Lachlan Musicman wrote:
> Hiram
>
> Sorry, I didn't explain myself properly.
>
> I *have* the GB installed on a VM, and I have snapshots for the devs to
> work on.
>
> What we are asking for is a front end to
>
> http://genomewiki.ucsc.edu/index.php/Building_a_new_genome_database
>
> ie, given a fasta file, a bed file and a ra file, upload into an *existing*
> instance.
>
> Cheers

> L.
>
> ------
> The most dangerous phrase in the language is, "We've always done it this
> way."
>
> - Grace Hopper
>

[Hiram Clawson]

Much more useful than attempting to install a local genome browser:

http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html
http://genome.ucsc.edu/goldenPath/help/hubQuickStart.html

Only takes a couple of plain text files, plus your track data
file in the big* formats and a few other formats. Note several
different types of examples in the above referenced documentation.

I have recently prototyped almost 50,000 genome assemblies into
assembly hubs:


http://genome-test.cse.ucsc.edu/~hiram/hubs/refseq/vertebrate_mammalian/vertebrate_mammalian.html

This is a prototype example, not ready for prime time yet, but already
quite useful.

--Hiram

On 10/22/15 7:25 PM, Lachlan Musicman wrote:
> Hiram,
>
> first I've heard of either of these two things ("x hubs"). What are they?
>
> cheers

> L.
>
> ------
> The most dangerous phrase in the language is, "We've always done it this
> way."
>
> - Grace Hopper
>

[Lachlan Musicman]

Hiram,

Thanks for the pointers. Unfortunately, as I have noted, we already have a stand alone installation of the GB.

Cheers

L.

------
The most dangerous phrase in the language is, "We've always done it this way."

- Grace Hopper

[Lachlan Musicman]

Hiram,

first I've heard of either of these two things ("x hubs"). What are they?

cheers

L.

------
The most dangerous phrase in the language is, "We've always done it this way."

- Grace Hopper

On 23 October 2015 at 13:23, Hiram Clawson <hi...@soe.ucsc.edu> wrote:

[Lachlan Musicman]

Hiram

Sorry, I didn't explain myself properly.

I *have* the GB installed on a VM, and I have snapshots for the devs to work on.

What we are asking for is a front end to

http://genomewiki.ucsc.edu/index.php/Building_a_new_genome_database

ie, given a fasta file, a bed file and a ra file, upload into an *existing* instance.

Cheers

L.

------
The most dangerous phrase in the language is, "We've always done it this way."

- Grace Hopper

On 23 October 2015 at 12:24, Hiram Clawson <hi...@soe.ucsc.edu> wrote: