san.p...@gmail.com
My scripts is as follows, since default python is 2.6.x:
/cm/shared/apps/python/2.7.5/bin/python2.7 /path/to/scaffold_builder_v2.2/scaffold_builder.py -q denovo_contigs.fa -r genomic_reference.fa -p test
I've installed MUMmer (downloaded from sourceforge) and copied put the nucmer executable in my /home/bin which is in my PATH. to the path. I've checked for all the dependencies listed in the MUMmer manual, all are in my PATH:
make (manual 3.79.1) - /usr/bin/make (3.81)
perl (manual 5.6.0) - /usr/bin/perl (v5.10.1)
sh (manual sh 1.14.7) - /bin/sh (4.1.2(1)-release (x86_64-redhat-linux-gnu))
csh (manual tcsh 6.10.00) - /bin/csh (6.17.00)
g++ (manual gcc 2.95.3) - /cm/shared/apps/gcc/4.4.6/bin/g++ (4.4.6)
sed (manual sed 3.02) - /bin/sed (4.2.1)
awk (manual awk 3.0.4) - /bin/awk (3.1.7)
ar (manual ar 2.9.5) - /usr/bin/ar (2.20.51.0.2-5.42.el6)
When I try to run it on the command line I just get the help message ans that's that. Any ideas why?
Many thanks.