Hi Karen,

HyPhy is problematic right now. Reports of failing on MAF input are the most recent on the public server, but the error you see is not outside of the scope of the problem (to my knowledge). This is the open ticket with more details:
https://trello.com/c/9TMF2aJl

I do not have an ETA for a correction.

Best!

Jen
Galaxy team

On 11/26/13 9:16 PM, Karen Miga wrote:

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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