[Bio-Linux] BioLinux 8 question - Adding and removing Paths - Velvet - correction

[Zain A Alvi]

Hi Tim and Tony,

Thank you so much for the detailed explanation of how $PATH work with Bio-Linux and how environments are set up in Bio-Linux. 

I tried to setup the paths to VelvetOptimiser and new Velvets in ZSH (~/.zshrc) and I've gotten command not found for VelvetOptimiser.

The lines that I added the are following two lines: 

export PATH=$PATH:/media/biolinux301/ab8abe44-b8f2-417c-81a5-276991c65d74/Velvet_Optimizer/VelvetOptimiser-2.2.5/
export PATH=$PATH:/media/biolinux301/ab8abe44-b8f2-417c-81a5-276991c65d74/Velvet_Optimizer/VelvetOptimiser-2.2.5/Velvet_Kmer303/

The first one is for VelvetOptimiser and the second one is for Velveth and Velvetg that was created for Kmer length of 303. 

If I try % VelvetOptimiser.pl then the output states  fg: no current job

I have follow up question in regards to aliases. VelvetOptimiser is designed specifically for look for Velveth and Velvetg and run them as it goes through each of the kmers. I am worried that it will seek the built in/old Velveth/g instead of the new compiled velveth/g.  It seeks the name velveth and velvetg respectively when it is executed in terminal. 

I've added the following alias terms in ~/.zshrc

alias velveth="/media/biolinux301/ab8abe44-b8f2-417c-81a5-276991c65d74/Velvet_Optimizer/VelvetOptimiser-2.2.5/Velvet_Kmer303/velveth_folder"
alias velvetg="/media/biolinux301/ab8abe44-b8f2-417c-81a5-276991c65d74/Velvet_Optimizer/VelvetOptimiser-2.2.5/Velvet_Kmer303/velvetg_folder"

If I type velveth or velvetg , I would receive an error of you do not have permission, which is strange as I am the administrator. I remember not being root could cause this occur. Could that be the reason here?

Now the strange part, is if I do sudo velveth then enter my password. Terminal will execute the built in/old velvet instead of the new one, which is strange.

Is there method for VelvetOptimiser to seek the  correct Velvet and without forcing sudo or having it override velvets that are built in.  Unfortunately renaming the newly compiled velvets is not an option as I far I can see so far.

Thank you again for the great help. I really appreciate it.

Kind regards,

Zain 



________________________________________
From: Tony Travis <tony.travis at minke-informatics.co.uk>
Sent: Wednesday, April 8, 2015 8:34 AM
To: bio-linux at nebclists.nerc.ac.uk
Subject: Re: [Bio-Linux] BioLinux 8 question - Adding and removing Paths - Velvet - correction

On 08/04/15 13:29, Tony Travis wrote:
> [...]
> Under Bio-Linux 8, you set up the environment for "zsh" in:
>
>   /etc/zshrc
>
> Which sources 'profile' fragments in:
>
>   /etc/zshrc.d/*

Hi, Tim.

Sorry, I meant:

  /etc/zsh/zshrc
  /etc/zsh/zshrc.d/*

Bye,

  Tony.

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