Hi Ross, 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.
Thanks again! Karen 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 > /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 > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > -- Karen H. Miga, PhD Postdoctoral Scholar University of California, Santa Cruz (831)459-5232
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
