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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