ou. If
possible you should
let galaxy handle the tool dependency installation and avoid using
system-installed binaries.
You can find more information about the tool installation process here:
https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/
Best,
Marius
On 24 March 2017 at 1
Subject: Re: [galaxy-dev] Dataset Generation Errors
Hi David,
this typically happens on older Galaxy versions (< 17.01) after installing new
or updated tools.
A galaxy restart should help.
Best,
Marius
On 23 March 2017 at 15:57, Lapointe, David
mailto:david.lapoi...@tufts.edu>> wro
I have installed the metaphlan tool ( dannon e951f9d38339) which installed with
the dependancies seemingly satisfied. I am getting an error
"This tool was disabled before the job completed" I can't determine why this
happens. In the handler log is this:
Tool 'toolshed.g2.bx.psu.edu/repos/danno
This site does not seem to be working for getting patches.
depot.galaxyproject.org
--
David Lapointe Ph.D.
Sr. Bioinformatics Specialist
Research Technology (RT)
Tufts Technology Services (TTS)
16 Dearborn Road
Somerville MA 02144
Phone: 617-627-5319
Fax: 617-627-3667
http://it.tufts.edu
From:
27;ll get the 16.07 release done too but juding by the way things look, it
won't be until the next month.
On Wed, Sep 14, 2016 at 11:23 AM, Lapointe, David
mailto:david.lapoi...@tufts.edu>> wrote:
Hi Enis,
Yes I figured what I was doing wrong. Using Cloudman to restart services
overwrote
e here:
https://wiki.galaxyproject.org/CloudMan/Services/Galaxy#Updating_Galaxy_source
We'll get the 16.07 release done too but juding by the way things look, it
won't be until the next month.
On Wed, Sep 14, 2016 at 11:23 AM, Lapointe, David
mailto:david.lapoi...@tufts.edu>> wrote
t getting back to you earlier.
On Thu, Aug 11, 2016 at 2:30 PM, Lapointe, David
mailto:david.lapoi...@tufts.edu>> wrote:
This is on Amazon I should add.
--
David Lapointe Ph.D.
Sr. Bioinformatics Specialist
Research Technology (RT)
Tufts Technology Services (TTS)
16 Dearborn Road
Somervill
This is on Amazon I should add.
--
David Lapointe Ph.D.
Sr. Bioinformatics Specialist
Research Technology (RT)
Tufts Technology Services (TTS)
16 Dearborn Road
Somerville MA 02144
Phone: 617-627-5319
Fax: 617-627-3667
http://it.tufts.edu
From: galaxy-dev
mailto:galaxy-dev-boun...@lists.galaxypr
I have a Cloudman instance up and running, but I would like to add SSL ( I
have a signed cert and key ) and productionize it. I see several methods
documented,but it's not clear which one is preferred: edit in place then
persist changes and restart (wiki/Cloudman/CustomizeGalaxyCloud) seems b
I am running the Docker for Mac (beta) and have a Galaxy, some what customized
via the Dockerfile, but otherwise out of the box. The owner in my mac storage
volume is me and within the docker , root, galaxy, or postgres. I've customized
the welcome.html and base.css.
root@5017ac030db9:/export#
Are there instance types which will not work for Galaxy/Cloudman on AWS? EBS
volumes for example.
Thanks,
David
--
David Lapointe Ph.D.
Sr. Bioinformatics Specialist
Research Technology (RT)
Tufts Technology Services (TTS)
16 Dearborn Road
Somerville MA 02144
Phone: 617-627-5319
Fax: 617-627-36
The Tophat2 entry screen does not list the reference genomes, however Bowtie2
does list them ( the ones I have in the bowtie2_indices.loc). The
bowtie2_indices.loc states that this file works for both Bowtie2 and Tophat2.
--
David Lapointe Ph.D.
Sr. Bioinformatics Specialist
Research and Geospat
I tried installing biopython and dependancies from the toolshed but this does
not seem to be functional even though these tools say INSTALLED. Is there
something that I should do that I missed? I sis better to installed them in
the regular python fashion?
--
David Lapointe Ph.D.
Sr. Bioinforma
I am having the same issue. The RHEL packages for atlas, blas, and lapack
are installed, but numpy 1.7 won't install, while numpy 1.9 seems to
install successfully.
--
David Lapointe Ph.D.
Sr. Bioinformatics Specialist
Research and Geospatial Technology Services
Tufts Technology Services (TTS)
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