problem using scaffold builder on the command line

[mndez...@gmail.com]

Hello,

when trying:
python /pathtoscaffol-cuilder/scaffolr_builder.py -q myqry.fasta -r myref.fasta -p myprefix
or same but specifying paths to files, the software outputs once and again the usage part from the readme file, or today I am getting this:
/home/apps/python/python-2.7.3/bin/python: can't find '__main__' module in '/home/apps/scaffold-builder/scaffold-builder-2.1'

Any ideas?

Thanks

[Geni]

Hi Celia,

Was your python installed correctly? I have looked online, and it seems that it is a python installation problem. If you are having trouble with the command line version, you can always use the scaffold builder web-server (http://edwards.sdsu.edu/scaffold_builder).


Best

[tsuc...@gmail.com]

I also have this peculiar problem when I try to run scaffold_builder using the following commands:
python scaffold_builder.py -q ../masucraContigs.fa -r ../ebi.fa -p assembly

In whichever combination I provide the commandline it always exists with this error:
Usage:
python scaffold_builder.py -q query_contigs.fna -r reference_genome.fna -p output_prefix [-t] [-i] [-a] [-b]
and a bunch of command options. I am not sure where I am going wrong.