I'm currently trying to scaffold with my contigs from a de novo assembly and the relevant paired-end reads. I've tried two programs so far: Scarpa (http://compbio.cs.toronto.edu/hapsembler/scarpa.html) and Opera (https://sourceforge.net/projects/operasf/files/OPERA-LG%20version%202.0.3/). I have downloaded both to my Unix Shell (so I'm able to use them in the command line). However, I've run into a problem. In both cases, I've been able to run the pre-processing steps (in scarpa, there are two scripts to use to get the files as they are needed and one such script to run using Opera), but when I get to the part of running the final script (i.e. 'scarpa' and 'OPERA-LG' for their respective programs), neither of the files/scripts are present in the folder to even use. Other scripts (i.e. the ones for pre-processing) are in that folder where the remaining programs should be, but the final script isn't there. Has anybody else encountered this previously and know how to fix it? Is it something wrong on my end or is it an issue with the program? I believe that I have all of the relevant dependencies that either program needs downloaded, so unless something has gone very wrong, that shouldn't be a problem.
Any help would be greatly appreciated!
So, I have solved my problem and am posting here in case somebody else someday comes across the same issue. On the day I was doing this, I was downloading several software packages, and seemed to skip over the 'make' step to compile the final scripts for these programs, thinking I had already done so because I did that for my other programs. If you come across the same issue as me for some reason (just doing too much at once and missing a step), try running 'make' after you've unzipped the program file and that should get everything working.