Prokka not running on Biolinux8

Question

[dago]

I installed prokka following the instruction provided by the author that you can fin here.

I installed all the dependencies as nicely explained here

However when I type

prokka

for testing it, i get

manager@bl8vbox[Documents]prokka 
zsh: command not found: prokka

These are my session information

manager@bl8vbox[Documents]ls   
barrnap-0.5  barrnap-0.5.tar.gz  hmmer-3.1b1  hmmer-3.1b1.tar.gz  minced-master  minced-master.zip  prodigal.v2_50.tar.gz  prodigal.v2_60.tar.gz  prokka-1.10  prokka-1.10.tar.gz
manager@bl8vbox[Documents] uname -a                            
Linux bl8vbox 3.13.0-37-generic #64-Ubuntu SMP Mon Sep 22 21:28:38 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

Do you have any idea what I do wrong?

[Ram]

Hi,

Could you maybe give the output of echo $PATH | tr ":" "\n" | grep -i "prokka" please? Thank you!

[Renesh]

set the path variable for prokka bin directory using export

[dago]

@RamsRS, thanks very much for your comment.

This is the result:

manager@bl8vbox[manager] echo $PATH | tr ":" "\n" | grep -i "prokka"            
manager@bl8vbox[manager] 

Basically, nothing...

[dago]

Thanks all for the reply and sorry for the late answer.

As you all got right the program is not in my PATH. But I guess I am to inexpert to fix this problem.

I added the followign directory to the file .bashrc:

manager@bl8vbox[manager] sudo find / -name prokka -print              [ 9:15AM]
[sudo] password for manager:
/home/manager/Documents/prokka-1.10/bin/prokka

sudo gedit .bashrc

I added the location above. Then I followed the isntruction here and I did the following:

manager@bl8vbox[manager] source ~/.bashrc                             [ 9:22AM]
/home/manager/.bashrc:16: command not found: shopt
/home/manager/.bashrc:24: command not found: shopt
/home/manager/.bashrc:108: command not found: shopt
/usr/share/bash-completion/bash_completion:35: parse error near `]]'
\[\e]0;\u@\h: \w\a\]${debian_chroot:+($debian_chroot)}\u@\h:\w\$  

\[\e]0;\u@\h: \w\a\]${debian_chroot:+($debian_chroot)}\u@\h:\w\$ echo $PATH

/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/cd-hit:/usr/lib/cd-hit:/home/manager/Documents/prokka-1.10/bin/prokka

\[\e]0;\u@\h: \w\a\]${debian_chroot:+($debian_chroot)}\u@\h:\w\$ prokka
zsh: command not found: prokka

Moreover if I quit the session and look for my avaialble path in a new session this is the result:

/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/cd-hit:/usr/lib/cd-hit:/home/manager/Documents/prokka-1.10/bin/prokka

So prokka is not in.

Any suggestion how I can add permanently more PATH?

[Ram]

It looks like the shell prompt display line in your ~/.zshrc has some problem. If you know how to find that line, comment it out. Else, paste your ~/.zshrc here and I'll help you out.

It would seem that the new terminal session PATH holds a pointer to prokka, though I wonder why you're running commands as sudo, especially the ~/.zshrc edit. You might wanna edit ~/.zshrc as a normal non super user.

EDIT: Updated to reflect the fact that @dago seems to be on zsh and not bash.

Answer 1

[Istvan Albert]

Linux / UNIX: Command Not Found Error and Solution

http://www.cyberciti.biz/faq/linux-unix-command-not-found-error-and-how-to-get-rid-of-it/

[Ram]

MTE. But OP's first link has instructions on export PATH. Should work, but doesn't. Curious.

Answer 2

[SES]

I think the issue is with the first set of instructions where you tried to set the PATH variable and likely overwrote the variable. Getting "zsh: command not found" when trying to execute a command seems to indicate that the shell can't find any command (note that prokka is written in Perl and has nothing to do with the error message).

I've never used biolinux, but you probably want to extend the PATH, not overwrite it, and this usually looks like:

export PATH=$PATH:/some/bio/dep

and not

export PATH=/some/bio/dep

I'm guessing something like the latter command was done, and it's no big deal, you can fix it by opening another shell (unless you edited your shell configuration).

Answer 3

[dago]

I think I managed to fix it.

On Ubuntu the file that has to be changed is /etc/environemt. In this file are listed the PATHS that are used.

I still did not manage to get the change in my path permanent, so everytime I have to

$ source /etc/environment

Update

I managed to keep the modified PATH permanent.

I simply did what I reported before and then I restarted the my system.

Thanks for your help.

[Ram]

The command to add a destination to your PATH and also to the current shell instance is:

echo 'export PATH=$PATH:/usr/local/bin'  >> ~/.bash_profile && source ~/.bash_profile