ah. you are right - I had not updated that older repository - I think I was
waiting for confirmation that the testtoolshed version worked - will do
shortly - thanks for pointing that out!
Try removing that one completely and then installing the test toolshed
version please? That should work until I get the main one updated in a few
hours.
On Mon, Dec 2, 2013 at 9:28 AM, Karen Miga <khmiga(a)soe.ucsc.edu> wrote:
Yes, I do all of my installs from the toolshed through the admin
menu,
however I did not use the "test toolshed..." I used the main. Ah ha -
maybe that was the issue?
Karen
On Sun, Dec 1, 2013 at 2:23 PM, Ross <ross.lazarus(a)gmail.com> wrote:
> Just to confirm, you used automated installation via the admin menu ->
> search and browse toolsheds -> test toolshed -> etc ?
> If you installed manually by downloading and unpacking the archive under
> your tools/ directory, then yes, there is no automation and you need to
> install the binary on your path. I believe the documentation explains this
> - if it's not clear please suggest some revisions ?
>
>
> On Mon, Dec 2, 2013 at 9:18 AM, Karen Miga <khmiga(a)soe.ucsc.edu> wrote:
>
>> 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.lazarus(a)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 <khmiga(a)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.lazarus(a)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
<khmiga(a)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.lazarus(a)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
>>
>
>
>
> --
> 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
--
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444