velvetoptimizer installation

[kmcarr]

thank you- velvet is installed on the server (I am not using velvet via galaxy or clcbio)-
I did not find contrib directory

I think for velvetoptimizer- bioperl is required- what are the steps for installing bioperl please

Have you tried this?

http://bit.ly/QCzeOd

[mmmm]

thank you- velvet is installed on the server (I am not using velvet via galaxy or clcbio)-
I did not find contrib directory

I think for velvetoptimizer- bioperl is required- what are the steps for installing bioperl please

[mastal]

You could try

$ module load velvet
$ contrib/VelvetOptimiser-2.2.4/VelvetOptimiser.pl

but
a) it would depend which version of VelvetOptimiser you have on your system

and b)
if you are using the command 'module load velvet'

I'm not sure what computer setup you are using, so you may not have
the velvet contrib directory.

Are you using something like Galaxy or CLCBIo to run velvet?

[mmmm]

velvet is already installed- which command to use in order to run velevtoptmizer perl script
I access velvet via
$
module load velvet
$velvetg

[mastal]

There should be a README file in the VelvetOptimizer directory.

I haven't used VelvetOptimiser, but as far as I can tell it's just a perl script that wraps around velvet, so you should be able to run it by just typing the full path to the location of the perl script, or else install it by adding the location of the VelvetOptimiser.pl script to your path.
.

By the way, if you have a copy of velvet, you probably have VelvetOptimiser in the contrib directory in velvet.

[mmmm]

thanks- but I am afraid that this did not work- which is the right command to try after this
• cd software-dir
• wget http://www.vicbioinformatics.com/Vel...r-2.2.5.tar.gz
• tar zxvf VelvetOptimiser-2.2.5.tar.gz

thanks for help

[sphil]

look at the 'INSTALL' but normally things go like:

./configure
make
make install (you may need 'su' priviledges for that)...

[mmmm]

I am trying to install velvet optimizer- I did the following:

• cd software-dir
• wget http://www.vicbioinformatics.com/Vel...r-2.2.5.tar.gz
• tar zxvf VelvetOptimiser-2.2.5.tar.gz

so now I have the unzipped directory (VelvetOptimizer-2.2.5./)- what should be done next please in order to use the software?