I am new to CLIMB and have started a GVL instance at Warwick to which I have ssh’ed remotely but I get error messages when trying to use Roary or do a brew search:
~$ roary
WARNING:root:could not open file ‘/etc/apt/sources.list.d/ppa_git_core_ppa_trusty.list’
WARNING:root:could not open file ‘/etc/apt/sources.list.d/ppa_galaxyproject_nginx_trusty.list’
WARNING:root:could not open file ‘/etc/apt/sources.list.d/apt_dockerproject_org_repo.list’
WARNING:root:could not open file ‘/etc/apt/sources.list.d/ppa_webupd8team_java_trusty.list’
No command ‘roary’ found, did you mean:
Command ‘roard’ from package ‘roaraudio’ (universe)
roary: command not found
~$ brew search
WARNING:root:could not open file ‘/etc/apt/sources.list.d/ppa_git_core_ppa_trusty.list’
WARNING:root:could not open file ‘/etc/apt/sources.list.d/ppa_galaxyproject_nginx_trusty.list’
WARNING:root:could not open file ‘/etc/apt/sources.list.d/apt_dockerproject_org_repo.list’
WARNING:root:could not open file ‘/etc/apt/sources.list.d/ppa_webupd8team_java_trusty.list’
No command ‘brew’ found, did you mean:
Command ‘brec’ from package ‘bplay’ (universe)
Command ‘qbrew’ from package ‘qbrew’ (universe)
brew: command not found
Another user on Birmingham has no problems with Roary on her GVL instance - can you advise?!
Hi Gemma - your problem is with the GVL image unfortunately, but its easily fixed. Birmingham and Cardiff are running updated GVL images, so instances there don’t suffer the same issue.
To fix, run the following command:
sudo chmod 644 /etc/apt/sources.list.d/*
This will restore the permissions on those apt source files to the correct ones.
Also, if this is a new instance, you might need to log out and log back in again. brew and roary are preinstalled on GVL so they should be found, unless you had started your SSH session before the instance had finished initializing completely.