How do you setup shareware locally so that make_fragment.pl can run secondary structure predictions locally?
Psipred is the easiest part, just download the package:http://bioinf.cs.ucl.ac.uk/software_downloads/
and follow the instruction.
As for Porter:http://distill.ucd.ie/porter/
you have to write an email to the author and probably sign a license.
SAM goes similar, there is just more setup to do in this case.
The major problem with these tools is that you have to set up paths to PsiBlast within their scripts.
So for example in the case of PsiPred you will have to edit runpsipred.local file which you find once you extract the archive you downloaded. In this file there is a couple of paths to be set, e.g:
# The name of the BLAST data bank
set dbname = /tools/DB/nr/nr
# Where the NCBI programs have been installed
set ncbidir = /tools/LEGACY/bin
# Where the PSIPRED V2 programs have been installed
set execdir = /tools/psipred/bin
# Where the PSIPRED V2 data files have been installed
set datadir = /tools/psipred/data
Of course you need a local installation of PsiBlast and >nr< sequence database, both can be downloaded from NCBI website. Note: the database takes about 11GB disk space. And be sure you downloaded the old "LEGACY" blast rather than the new C++ one.