Installing software on Ubuntu as non-root

Question

I've been stuck on a problem for two days now where the software I'm trying to install will not proceed unless I make a separate user which is non-root.

Keep in mind I'm a big linux noob and not very experienced with the OS.

• I make a user called "smrtanalysis" in a group called "smrtanalysis".
• I put him in the sudoers file.
• I made a folder called smrtanalysis in my home/nick/ directory
• I downloaded the software from the PacBio website and put the .run files into this directory I noted above.
• I used chmod 777 and chown (to user smrtanalysis) on the directory noted above, and the .run file

• I logged into smrtanalysis user by su smrtanalysis, password, and typed

  ./smrtanalyis-2.2.0.133377.run

the file runs, but then aborts with the following error message:

We recommend running this script as a designated SMRT Analysis user (e.g. smrtanalysis) who will own all smrtpipe jobs and daemon processes.

Current user is 'root' (primary group: root)

Installing as 'root' is currently not supported Switch to the desired user and restart the install. Aborting installation...

Here is the install documentation: https://github.com/PacificBiosciences/SMRT-Analysis/wiki/SMRT-Analysis-Software-Installation-v2.2.0

It seems pretty straightforward but I can't seem to get it working. If you guys look at the install docs, you'll probably be able to tell me what I'm doing wrong.

Thanks for any help!

Regards, Nick

Answer 1

change

SMRT_ROOT=/opt/smrtanalysis

on

SMRT_ROOT=/home/nick/smrtanalysis

the rest should be easy.

Be very careful installing binaries from internet, make sure you're confident in the source.

Answer 2

Just don't use root for that, you ran the script as root by accident.

(update: pacbio team can help from the github page at https://github.com/PacificBiosciences/SMRT-Analysis/issues as well.)