(1) Clustalw:  The program completes without error and produces an empty file and a log file that states "/bin/sh: 1: clustalw2: not found"

Searching around a bit I am not seeing clustalw2 previously installed.  I am happy to do it if need be, however, I wanted to check in and see if I am overlooking the directory or an easy fix.

 

If I do need to install clustalw,  I would prefer to use clustalw-omega, but was not sure if I needed to script a brand new wrapper or if I could use the previous one that came with galaxy image.

(2) HyPhy:  The cloud the link was initially broken.  I changed it to the correct path:

sudo ln -sfn /mnt/galaxy/tools/hyphy/default /mnt/galaxy/galaxy-app/tool-data/HYPHY

I am using a fasta alignment file of 6 protein sequences (566 AA each) as a test case (*also fails with nucleotide alignments).

 

It runs briefly and then issues an error statement "Single Alignment Analyses Segmentation fault (core dumped)".

Thank you in advance,

Karen