Thanks for your email. I have clustalw2 working now - I installed the
clustal repository (as suggested) from toolshed and then installed the
clustalw2 binaries in our mnt/galaxy/tools/bin.
On Wed, Nov 27, 2013 at 12:46 AM, Ross <ross.laza...@gmail.com> wrote:
> 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
> 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,
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Karen H. Miga, PhD
University of California, Santa Cruz
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