Hi Matthias
No, the twobit-files are not mandatory for trackster. They are only
required if you want to zoom into the nucleotide level.
Also, though, I am not sure, and I recommend to check this with your
legal department, but I have been under the impression that the tool
'faToTwoBit' can be built from the "kent/src/utils" source code
directory, which is freely available for all uses, isn't-it?
Regards, Hans-Rudolf
On 10/17/2017 04:29 PM, Matthias Enders wrote:
Hi Hans,
actually we are a company and the UCSC Genome Browser is not freely available
for us. As you pinpointed me to the website:
https://galaxyproject.org/visualization-setup/
There is an link to USCS utilities (for creating twobitfiles)
(http://hgdownload.cse.ucsc.edu/admin/exe/)
Actually this tools are also under license agreements, that permits free
commercial download or usage.
If I understand it correctly the twobit-files are mandatory for trackster,
implicating that we have to buy licenses for using UCSC Genome Browser and/or
Trackster?
If yes: Are there any attempts to build in or rebuild this utilities, so the full project
with all parts "remains" compatible with AFL3 license?
Mit freundlichen Grüßen
Matthias Enders
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Hans-Georg Lembke KG
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-----Ursprüngliche Nachricht-----
Von: Hans-Rudolf Hotz [mailto:h...@fmi.ch]
Gesendet: Dienstag, 17. Oktober 2017 10:33
An: Matthias Enders <m.end...@german-seed-alliance.de>;
galaxy-dev@lists.galaxyproject.org
Betreff: the future of trackster - was: galaxy-dev Digest, Vol 136, Issue 8
Hi Matthias
We had a Birds of a Feather session about (the future of) Trackster at the
recent galaxy community conference in Montpellier. Though, as far as I know (I
might be wrong), this didn't result in any no active development on the
Trackster code.
What kind of functionality do you miss? It might be worth rising an issue on
github (https://github.com/galaxyproject/galaxy/issues) ?
Personally, I consider Trackster and the option to display data at the
UCSC genome browser as two different pairs of shoes:
- Trackster is a easy option to look at your data quickly. It is
particular useful, if you work with non-model organisms
- the display of your data at UCSC is handy, if you want to visually
compare it with all the available UCSC tracks. However, keep in mind,
unless you are using a local copy of the UCSC gemome browser, the data
will leave your local network.
WRT tutorial: Have you seen these pages:
https://galaxyproject.org/learn/visualization/
https://galaxyproject.org/visualization-setup/
Regards, Hans-Rudolf
PS: I took the freedom to change the subject line for easier searching
in the future
On 10/16/2017 03:50 PM, Matthias Enders wrote:
Dear Galaxy Dev List,
we currently searching for a good Genome Browser. As we run a local galaxy instance, we
noticed the integrated GTB ("Galaxy Track Browser").
So my question is: Is there a roadmap for further support / development of the
GTB?
Or will it perhaps get replaced/deprecated in the near future (we read a lot of
UCSC Genome Browser - Galaxy - Integration)?
Another question would be on good sources/tutorials/manuals for configuring and
setup for the GTB.
Mit freundlichen Grüßen
Matthias Enders
-----------------------------------------------------------------------
GERMAN SEED ALLIANCE GmbH
c/o Norddeutsche Pflanzenzucht
Hans-Georg Lembke KG
Hohenlieth, 24363 Holtsee
Tel.: +49 (0)4351/ 736-189
Fax: + 49 (0)4351/ 736-271
Mobil: +49 (0)151/ 14247360
Email: m.end...@german-seed-alliance.de
Firmensitz Köln
Amtsgericht Köln, HRB 73844
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