Hi Ross,

   I did not detect any type of auto-install (?)  After installing from
toolshed I did not find the binary under the /mnt/galaxy/shed_tools/
toolshed.g2.bx.psu.edu/repos/   (or /mnt/galaxy/tools or
/mnt/galaxy/tools/bin for that matter).  Am I looking in the wrong place?


On Sun, Dec 1, 2013 at 2:00 PM, Ross <ross.laza...@gmail.com> wrote:

> 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

Karen H. Miga, PhD

Postdoctoral Scholar
University of California, Santa Cruz
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