Hi, Karen - how did you install clustalw? 
If not already done, can you please try installing the clustal repository owned by fubar from the test toolshed through your Galaxy admin interface - search/browse toolsheds? Please let me know how you go and if there's a problem I'll try to fix it for you. I think there's a clustal omega tool too but it's not one of mine. As far as I know my clustal repository should install cleanly on a CloudMan instance.

Sorry but we'll have to wait to from someone who knows about HyPhy.

Hello - I am running to errors when trying to run Clustalw and HyPhy on our cloudman instance.

(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

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