Music - Problems With Installing In Ubuntu And Where Do We Start With Loading Into Galaxy?

Question

[Nicholas Blackburn]

I have spent some time trying to get MuSiC to work through Ubuntu. The initial installation command:

wget -q -O - https://apt.genome.wustl.edu/ubuntu/files/install.sh | sudo bash

sits for quite some time not achieving anything. So I attempted to follow the repository linking commands but at

wget https://apt.genome.wustl.edu/ubuntu/files/genome-institute.asc

the terminal tries to connect to apt.genome.wustl.edu repeatedly, with the connection timing out each time.

(This all may be a problem at my end, our IT guys can't offer any support for Ubuntu as it's not supported by our University so I'm very much trying to figure it out as I go)

Alternatively we have Galaxy running on our local server. How do we go about loading MuSiC into Galaxy?

Regards,

Nicholas Blackburn | PhD Candidate

Tasmanian Inherited Cancer Centre

Menzies Research Institute Tasmania

[Bpow]

This is at a much earlier than installation since you cannot even download the install script. Perhaps the https port is blocked by a firewall?

You could try downloading the file with

wget http://apt.genome.wustl.edu/ubuntu/files/install.sh

(note 'http' instead of 'https') If that works, then you would have a chance of being able to install in a less-automated manner. Unfortunately, you would have to run the commands of the script manually or at least edit the file (it wants to download the repository signing key using https-- which is a good idea since adding it will list items signed with that key as "trusted" by apt).

Answer 1

[Cyriac Kandoth]

Glad you got the installation to work. We have not yet put the tool config files on the public toolshed. But you can find these XML files in the source code, for each Perl module. If you followed the recommended installation process, then the code should be down this path:
/usr/share/perl5/Genome/Model/Tools/Music/

Alternatively, you can directly download a source code tarball from our APT repository:
http://apt.genome.wustl.edu/ubuntu/pool/main/g/genome-music/genome-music_0.4.1-1.tar.gz

~Cyriac

[Nicholas Blackburn]

Thanks Cyriac, much appreciated.

Answer 2

[Istvan Albert]

It seems that the url in question may not have its certificate in order so the wget command may fail. This below worked for me

wget --no-check-certificate https://apt.genome.wustl.edu/ubuntu/files/genome-institute.asc

so perhaps try passing the --no-check-certificate parameter to wget

As for Galaxy integration, first you would need to make sure that it runs at the command line, Galaxy is an interface to invoke programs that are installed on a given computer.

[Nicholas Blackburn]

Thanks for the response Istvan! I was hopeful that would work, but unfortunately same result. Any other suggestions?

nicholas@nicholas-MacBookPro:~$ wget --no-check-certificate https://apt.genome.wustl.edu/ubuntu/files/genome-institute.asc

--2012-12-03 14:03:20-- https://apt.genome.wustl.edu/ubuntu/files/genome-institute.asc Resolving apt.genome.wustl.edu apt.genome.wustl.edu)... 128.252.233.45 Connecting to apt.genome.wustl.edu apt.genome.wustl.edu)|128.252.233.45|:443... failed: Connection timed out. Retrying.

--2012-12-03 14:04:24-- (try: 2) https://apt.genome.wustl.edu/ubuntu/files/genome-institute.asc Connecting to apt.genome.wustl.edu apt.genome.wustl.edu)|128.252.233.45|:443... failed: Connection timed out. Retrying.

[nnutter]

The SSL certificate should be fine but we have found that a lot of sites use an HTTP proxy that doesn't work, or needs to be configured, for HTTPS connections particularly for certain tools like wget and APT.

Answer 3

[Nicholas Blackburn]

HI all,

Thanks for the tips. The solution ended up being 'take the laptop home away from the nasty university proxy and install'. Running smoothly now.

Cheers,

Nick

[nnutter]

You could also just use http:// instead of https://. The only part that you really want to be careful about security-wise is to trust that you download our key since that is what is used to verify the authenticity of the packages we release.

Answer 4

[tnabtaf]

In this MuSIC paper (http://genome.cshlp.org/content/22/8/1589) the authors say:

and integration of MuSiC into Galaxy (http://usegalaxy.org) is also available.

Try contacting the authors. It does not appear to be in the Galaxy Tool Shed.