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
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,
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
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
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
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.laza...@gmail.com wrote:
Just to confirm, you used automated installation via
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
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
Hi Karen,
HyPhy is problematic right now. Reports of failing on MAF input are the
most recent on the public server, but the error you see is not outside
of the scope of the problem (to my knowledge). This is the open ticket
with more details:
https://trello.com/c/9TMF2aJl
I do not have an
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
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