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?
2 answers
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.
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..
•
written
by
Antonio R. Franco
Log in to answer this question.
-
Download and install StringTie
written by SKY •
-
Salmon installation error
written by kousi31 •
-
Memsat-SVM: error running PSI-BLAST
written by Thomas B. •
-
I can't install HiC-Pro
written by rahman.samir33 •
-
How to add tophat and bowtie to the path?
written by mirza
-
How to add tophat and bowtie to the path?
written by mirza
-
run softwares tophat
written by zh.khodadadi •
-
Tutorial: Installation VMD on LINUX_64
written by Hassan Rasouli •
-
using featureCounts in command line
written by zizigolu
-
no happen when runing tophat in fedora
written by zizigolu
Hi,
Did you also copy it in the bin folder and change chmod?
Why download VelvetOptimizer separately? You can just download the latest velvet package, and VelvetOptimizer is part of it.
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.
Like I said before, you don't need to download VelvetOptimizer, it's already part of the velvet package. You
cdinto the correct directory, I believe something likecontrib/VelvetOptimizer, and from there you can directly run the scriptperl VelvetOptimizer.pl.