VelvetOptimizer:Error in running the program

Question

[mirza]

Hi,

I downloaded the package VelvetOptimiser-2.2.5.tar.gz and placed it in Downloads/softwares and unzipped/untarred it using the command lines

% cd $Downloads/softwares
% sudo tar zxvf /Downloads/softwares/VelvetOptimiser-2.2.5.tar.gz

Now I have VelvetOptimiser-2.2.5 folder in my location i.e. Downloads/softwares/VelvetOptimiser-2.2.5 and have all the file i.e.

CHANGELOG  INSTALL  LICENSE  README  sng2.fastq  VelvetOpt  VelvetOptimiser.pl

But, when I am trying to run it using % VelvetOptimiser.pl

Result- "command not found"

What am I missing?

[Sissi]

Hi,

Did you also copy it in the bin folder and change chmod?

[Adrian Pelin]

Why download VelvetOptimizer separately? You can just download the latest velvet package, and VelvetOptimizer is part of it.

[mirza]

Hello everyone and thanks for your replies. I am new to ubuntu or for the matter to linux environment. So, plz help me out.

@Adrian- I already had Velvet_1.2.10 installed in my system, so I downloaded the velvetoptimizer only.

@Sissi- No I didn't

@SES-what command line I need to use, plz help me out

@Antonio- thanks, it worked.

[Adrian Pelin]

Like I said before, you don't need to download VelvetOptimizer, it's already part of the velvet package. You cd into the correct directory, I believe something like contrib/VelvetOptimizer, and from there you can directly run the script perl VelvetOptimizer.pl.

Answer 1

[SES]

You need to have that directory in your path or it won't work, and neither will moving the script. Unfortunately, it has no build/install system so it has to be used in place. Or, you can type "perl" followed by the path to the script and it will work.

Answer 2

[Antonio R. Franco]

If you don't know how to export the path or how to create a symbolic link of your binaries in an accessible directory of your path, you can run the program this way (that is by writing a "."). In this case you need to be in the same directory where the program is

$./VelvetOptimizer..