Hi Ross,

  That is listed as "tool_dependency_dir = /mnt/galaxy/tools" in my
universe_wsgi.ini file, and that did not contain a clustalw directory
either before or after the toolshed install.

Karen


On Sun, Dec 1, 2013 at 2:10 PM, Ross <ross.laza...@gmail.com> wrote:

> yes. In universe_wsgi_ini you have a definition for tool_dependency_dir -
> that's why I wrote:
>  [tool_dependency_directory]/clustalw/2.1/fubar/clustalw/76de6971a0de/  as
> the path - the funny numbers are the repository revision number - that's
> where the toolshed installs the binary and the env.sh file needed for the
> tool to find it.
>
>
>
> On Mon, Dec 2, 2013 at 9:08 AM, Karen Miga <khm...@soe.ucsc.edu> wrote:
>
>> 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?
>>
>> Karen
>>
>>
>> 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
>> (831)459-5232
>>
>
>
>
> --
> Ross Lazarus MBBS MPH;
> Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
> http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ
>



-- 
Karen H. Miga, PhD

Postdoctoral Scholar
University of California, Santa Cruz
(831)459-5232
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