Re: galaxy-dev Digest, Vol 136, Issue 8

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Re: galaxy-dev Digest, Vol 136, Issue 8

M_Enders
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: [hidden email]

Firmensitz Köln
Amtsgericht Köln, HRB 73844
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
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the future of trackster - was: galaxy-dev Digest, Vol 136, Issue 8

Hans-Rudolf Hotz
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: [hidden email]
>
> Firmensitz Köln
> Amtsgericht Köln, HRB 73844
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>    https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>    http://galaxyproject.org/search/
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/
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Re: the future of trackster - was: galaxy-dev Digest, Vol 136, Issue 8

M_Enders
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
-----------------------------------------------------------------------


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: [hidden email]

Firmensitz Köln
Amtsgericht Köln, HRB 73844

-----Ursprüngliche Nachricht-----
Von: Hans-Rudolf Hotz [mailto:[hidden email]]
Gesendet: Dienstag, 17. Oktober 2017 10:33
An: Matthias Enders <[hidden email]>; [hidden email]
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: [hidden email]
>
> Firmensitz Köln
> Amtsgericht Köln, HRB 73844
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>    https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>    http://galaxyproject.org/search/
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/
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Re: the future of trackster - was: galaxy-dev Digest, Vol 136, Issue 8

Hans-Rudolf Hotz
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
> -----------------------------------------------------------------------
>
>
> 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: [hidden email]
>
> Firmensitz Köln
> Amtsgericht Köln, HRB 73844
>
> -----Ursprüngliche Nachricht-----
> Von: Hans-Rudolf Hotz [mailto:[hidden email]]
> Gesendet: Dienstag, 17. Oktober 2017 10:33
> An: Matthias Enders <[hidden email]>; [hidden email]
> 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: [hidden email]
>>
>> Firmensitz Köln
>> Amtsgericht Köln, HRB 73844
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>     https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>     http://galaxyproject.org/search/
>>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/
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Re: the future of trackster - was: galaxy-dev Digest, Vol 136, Issue 8

M_Enders
Hi Hans,

your right, I´ve checked this. The utils are free and the folder on GITHub contains the tools needed. Perhaps it´s an idea to change the link on the website (https://galaxyproject.org/visualization-setup/) from here ("http://hgdownload.cse.ucsc.edu/admin/exe/")
to github? ("https://github.com/ucscGenomeBrowser/kent/tree/master/src/utils")

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: [hidden email]

Firmensitz Köln
Amtsgericht Köln, HRB 73844

-----Ursprüngliche Nachricht-----
Von: Hans-Rudolf Hotz [mailto:[hidden email]]
Gesendet: Dienstag, 17. Oktober 2017 16:50
An: Matthias Enders <[hidden email]>; [hidden email]
Betreff: Re: AW: the future of trackster - was: galaxy-dev Digest, Vol 136, Issue 8

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
> ----------------------------------------------------------------------
> -
>
>
> 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: [hidden email]
>
> Firmensitz Köln
> Amtsgericht Köln, HRB 73844
>
> -----Ursprüngliche Nachricht-----
> Von: Hans-Rudolf Hotz [mailto:[hidden email]]
> Gesendet: Dienstag, 17. Oktober 2017 10:33
> An: Matthias Enders <[hidden email]>;
> [hidden email]
> 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: [hidden email]
>>
>> Firmensitz Köln
>> Amtsgericht Köln, HRB 73844
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this and other
>> Galaxy lists, please use the interface at:
>>     https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>     http://galaxyproject.org/search/
>>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/
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Re: the future of trackster - was: galaxy-dev Digest, Vol 136, Issue 8

Nicola Soranzo-2
In reply to this post by Hans-Rudolf Hotz
According to the website, only UCSC Genome Browser and Blat require a
commercial license.

Cheers,
Nicola

On 17/10/17 15:50, Hans-Rudolf Hotz wrote:

> 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
>> -----------------------------------------------------------------------
>>
>>
>> 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: [hidden email]
>>
>> Firmensitz Köln
>> Amtsgericht Köln, HRB 73844
>>
>> -----Ursprüngliche Nachricht-----
>> Von: Hans-Rudolf Hotz [mailto:[hidden email]]
>> Gesendet: Dienstag, 17. Oktober 2017 10:33
>> An: Matthias Enders <[hidden email]>;
>> [hidden email]
>> 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: [hidden email]
>>>
>>> Firmensitz Köln
>>> Amtsgericht Köln, HRB 73844
>>> ___________________________________________________________
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>>     https://lists.galaxyproject.org/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>     http://galaxyproject.org/search/
>>>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>  https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/
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Re: the future of trackster - was: galaxy-dev Digest, Vol 136, Issue 8

Hans-Rudolf Hotz
In reply to this post by M_Enders


On 10/17/2017 05:02 PM, Matthias Enders wrote:
> Hi Hans,
>
> your right, I´ve checked this. The utils are free and the folder on GITHub contains the tools needed. Perhaps it´s an idea to change the link on the website (https://galaxyproject.org/visualization-setup/) from here ("http://hgdownload.cse.ucsc.edu/admin/exe/")
> to github? ("https://github.com/ucscGenomeBrowser/kent/tree/master/src/utils")

like the whole galaxy project, the Galaxy hub pages are a community
effort. So feel free to improve the page yourself by making a adding the
github page as a second resource for the faToTwoBit tool.


Hans-Rudolf


>
> 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: [hidden email]
>
> Firmensitz Köln
> Amtsgericht Köln, HRB 73844
>
> -----Ursprüngliche Nachricht-----
> Von: Hans-Rudolf Hotz [mailto:[hidden email]]
> Gesendet: Dienstag, 17. Oktober 2017 16:50
> An: Matthias Enders <[hidden email]>; [hidden email]
> Betreff: Re: AW: the future of trackster - was: galaxy-dev Digest, Vol 136, Issue 8
>
> 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
>> ----------------------------------------------------------------------
>> -
>>
>>
>> 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: [hidden email]
>>
>> Firmensitz Köln
>> Amtsgericht Köln, HRB 73844
>>
>> -----Ursprüngliche Nachricht-----
>> Von: Hans-Rudolf Hotz [mailto:[hidden email]]
>> Gesendet: Dienstag, 17. Oktober 2017 10:33
>> An: Matthias Enders <[hidden email]>;
>> [hidden email]
>> 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: [hidden email]
>>>
>>> Firmensitz Köln
>>> Amtsgericht Köln, HRB 73844
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