Thanks Peter. You guessed correctly, I tried
https://toolshed.g2.bx.psu.edu/view/clustalomega/clustalomega ... I'm back
to using the command line ;-)
cheers,
Isabelle
On 10/7/14 1:45 AM, "Peter Cock" wrote:
>On Tue, Oct 7, 2014 at 1:47 AM, Isabelle Phan
> wrote:
>&g
Hello,
I installed clustalomega from the galaxy main toolshed using the admin
interface of our local galaxy install. When I run the tool, I get this
message:
Dataset generation errors
Dataset 55: co_alignment.fasta
Tool execution generated the follow
section in your tool it should work.
>
>Good luck!
>Bjoern
>
>
>Am 04.06.2014 01:17, schrieb Isabelle Phan:
>> I am using env.sh to manage my tool dependencies:
>>
>> # tool_dependency_dir/hhsuite/2.0.16/env.sh
>> export HHPRED_DIR=/opt/galaxy-dist/tool_depend
I am using env.sh to manage my tool dependencies:
# tool_dependency_dir/hhsuite/2.0.16/env.sh
export HHPRED_DIR=/opt/galaxy-dist/tool_dependencies/hhsuite/default
export HHLIB=${HHPRED_DIR}/lib/hh
export PATH=${HHPRED_DIR}/bin:${HHLIB}/scripts:$PATH
Galaxy is not sourcing it. I have to manually
wxr-xr-x@ 6 iphan SBRI\Domain Users 204B May 30 13:20 lib/
thanks,
Isabelle
On 6/2/14 10:50 AM, "Isabelle Phan"
wrote:
>Hello Dave,
>
>I got interrupted before I could reply to the second suggestion from
>Jorrit:
>
>> Not sure about specifying the ab
the cause of this issue, could you provide
>the output of the following two commands?
>
>ls -lh tool_dependencies/hhsuite/
>ls -lh tool_dependencies/hhsuite/default/
>
> --Dave B.
>
>On Mon 02 Jun 2014 01:29:44 PM EDT, Isabelle Phan wrote:
&g
I tried
hhsuite
and that had no effect.
I.
--
Message: 3
Date: Sat, 31 May 2014 03:51:55 +0200
From: Bj?rn Gr?ning
To: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] tool dependencies fail
Message-ID: <538935bb.7020...@gmail.com>
Content-Type: text/plain
Hello,
I'm following "Managed Tool Dependencies" to the letter and still can't
get Galaxy to find the executable. Is this page
https://wiki.galaxyproject.org/Admin/Config/ToolDependencies up to date?
If yes, what am I doing wrong?
Any help greatly appreciated!
# universe_wsgi.ini
# I also tried
nt AMI, we do not currently
have support for that type of instances - maybe down the line.
Nonetheless, in the coming new version Galaxy Cloud (currently being tested),
the application will be able to automatically scale the size of the cluster
based on the current workload.
--
Isabel
lle
> -Original Message-
> From: Enis Afgan [mailto:eaf...@emory.edu]
> Sent: Friday, March 11, 2011 4:42 PM
> To: Isabelle Phan
> Cc: galaxy-dev@lists.bx.psu.edu; Gowthaman Ramasamy
> Subject: Re: [galaxy-dev] testing updates on Galaxy CloudMan
>
> Hi
> Isabelle
y would appreciate a response.
Isabelle
--
Isabelle Phan, DPhil
Seattle Biomedical Research Institute
+1(206)256 7113
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Hello Sarah,
(my galaxy-dev account is broken, read your post on nabble)
You need to disable filter-with=gzip in order to set debug=False
But in any case, I have not seen a difference in the log, so my take is that
galaxy only ever runs in debug mode.
Isabelle
___
--
Isabelle Phan, DPhil
Seattle Biomedical Research Institute
+1(206)256 7113
> -Original Message-
> From: Isabelle Phan
> Sent: Wednesday, March 09, 2011 6:21 PM
> To: 'galaxy-dev@lists.bx.psu.edu'
> Cc: Andy Leonard; Gowthaman Ramasamy
> Subject: galaxy-cloud di
laxy does not have this issue, only the cloud instance.
Since this is a total blocker, any hint is *very* gratefully received,
Isabelle
--
Isabelle Phan, DPhil
Seattle Biomedical Research Institute
+1(206)256 7113
___
Please keep all replies
Hello,
Has anybody written a mosaik reference-alignment/assembly tool for galaxy that
they would be willing to share?
Thanks,
Isabelle
--
Isabelle Phan, DPhil
Seattle Biomedical Research Institute
+1(206)256 7113
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