Running scaffold builder on local linux machine

[sesh...@gmail.com]

I'm trying to run scaffold_builder on my local linux machine, however when I try it on the test dataset with this command

python ../scaffold_builder.py -q ecoli_Contigs.fna -r ecoli_reference.fasta -p test

it prints the help message and nothing else.

Do you have any insight into what might be going wrong? I am running the python script included in the v2.1 download.

http://sourceforge.net/projects/scaffold-b/files/latest/download

Sesh

[Geni]

Hi Sesh,

Your command line looks fine. However, you might be missing some of the dependencies.

Do you have nucmer installed? What is the version of your default python?

Take care

[sesh...@gmail.com]

The issue was with the install of nucmer not finding perl

bash: /usr/local/bin/nucmer: /usr/local/bin/perl: bad interpreter: No such file or directory

Fixed the problem by setting PATH to use a local installation of nucmer instead.

[san.p...@gmail.com]

I'm having the same problem. How did you figure out that the issue was nucmer not finding perl?

[sesh...@gmail.com]

It has been a long time since I did this, but I think the path to perl given in the output "/usr/local/bin/perl” was not the path to the perl installation as given by which perl "/usr/bin/perl"