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

[Zain A Alvi]

Dear Sir or Madam,


I hope this reaches you well. I am trying to add the Velvet (a custom version with Kmer value of 303, and another version that Velvet that was made up to 191) and VelvetOptimiser to path. In my findings with BioLinux 8's documentation, I found Velvet was pre-installed with BioLinux, which is great and useful. Unfortunately, the Kmer value is too low for our needs.


I was wondering where exactly is the file to edit the path to this tool. I have tried export PATH=/dir/:$PATH , but I rather know where exactly is the file is located to edit.  I have taken a look into $HOME/.bashrc (or ~/.bashrc) via gedit to no avail as well.


Also I found the tools (Velvet and more tools) to be found in /usr/bin/ folder but they can't be replaced and they are found repeatedly in the X11 folders within them as well.


I was wondering if you could kindly help in finding on correct folder and adding files to $PATH to alleviate this situation and have my higher kmer version of Velvet be used by VelvetOptimiser.


Sincerely,


Zain Alvi


---

zain.alvi at student.shu.edu

Ph. D. Candidate in Molecular Bioscience

Seton Hall University

Ph: (973) 710-7149


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