Hi Karen,
Glad to hear it worked for you. It the tool auto-installs correctly, it
downloads and unpacks the binary under
[tool_dependency_directory]/clustalw/2.1/fubar/clustalw/76de6971a0de/ so
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)
are removed?


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!
> 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
>>
>>
>>
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