Pre-installed software on GVL


#1

I have launched a GVL instance using the instructions here ( How to: Launching a GVL instance ), it is a user instance running at Swansea and according to the dashboard everything is running fine. I was expecting more software to be pre-installed but I can’t run, eg, prokka or snippy, and I also don’t have brew. Is there something else I need to do to the instance to get those working? I can run bwa and samtools.

My $PATH looks like this: /home/ubuntu/bin:/home/ubuntu/.local/bin:/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/mnt/galaxy/tools/bin:/usr/lib/postgresql/9.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin


#2

Hi Liz,

That sounds like the instance has not finished building correctly. The following might resolve this:

1/ If you log via ssh
2/ Run sudo apt update
3/ Run sudo apt upgrade
4/ Restart the instance from the Bryn dashboard.

We are in the process of updating the GVL to resolve these build issues. We should be rolling out a new build over the next week. Sorry for any inconvenience.

All the best,
Sion


#3

Hi Sion,

Yes, that fixed it. Thanks!


#4

No problem, glad I could help!


#5