Glad to hear it worked for you. It the tool auto-installs correctly, it
downloads and unpacks the binary under
the binary you installed manually should not ever be needed by the toolshed
version - try moving it off your path - the tool should continue to work
correctly? Apologies - I should have suggested removing any manual
installations and their corresponding tool_conf.xml entries before using
the automated installation - the tool shed installation doesn't prevent you
from having 2 versions of the same tool in your tool menu - until those
manually installed ones (which may depend on clustalw2 being on the path)
On Mon, Dec 2, 2013 at 8:36 AM, Karen Miga <khm...@soe.ucsc.edu> wrote:
> 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!
> 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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