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 in
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 wrote:
> Hi, Karen - how did you
Hello,
I would like to use hmmer on our cloudman instance. However, when I
install I am only finding a wrapper for hmmpress. There was some
conversation about this back in 2012 (
http://gmod.827538.n3.nabble.com/Missing-tool-previews-in-tool-shed-e-g-hmmer-xml-td3838635.html).
I installed
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 wrote:
>
>>
le needed for the
> tool to find it.
>
>
>
> On Mon, Dec 2, 2013 at 9:08 AM, Karen Miga 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/
>
ion explains this
> - if it's not clear please suggest some revisions ?
>
>
> On Mon, Dec 2, 2013 at 9:18 AM, Karen Miga wrote:
>
>> Hi Ross,
>>
>> That is listed as "tool_dependency_dir = /mnt/galaxy/tools" in my
>> universe_wsgi.ini fi
t; should provide sample entries for the Galaxy data tables that this tool
> must use. I'm not sure of the layout of this table for this particular
> tool, but if you discover what it should be, you can manually add them into
> a file named hmmdb.loc in the ~/tool-data directory in y
Hello,
I am trying to use phyloviz on the cloud/Galaxy cloudman. Unfortunately,
I am unable to save the visualization using the save/disk icon on the right
hand side of the banner. Any help would be appreciated.
Karen
___
Please keep all
restart my cloud instance? Should I get
instant feedback with the invalid hmmer.xml is valid, do I need to
reinstall?
Karen
On Mon, Dec 2, 2013 at 3:51 AM, Peter Cock wrote:
>
>
>
> On Mon, Dec 2, 2013 at 4:50 AM, Karen Miga wrote:
>
>> Hi Greg,
>>
>>Thanks f
Hello,
I am currently unable to install a number of tools from toolshed to our
cloud instance. Unfortunately, this pops up for quite a few tools (I am
currently trying to install cuffmerge, but I see this again and again).
Any help would be appreciated!
I am seeing the following error:
URL:
ht
Hello,
I am unable to reach my cloudman console. I was trying to reboot the
master. The instance is running on AWS console with no error, I just have
no way of access the admin console to terminate or figure out the error
through cloud launch. Further, I am now unable to launch a new instance.
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