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: [email protected] Firmensitz Köln Amtsgericht Köln, HRB 73844 -----Ursprüngliche Nachricht----- Von: Hans-Rudolf Hotz [mailto:[email protected]] Gesendet: Dienstag, 17. Oktober 2017 16:50 An: Matthias Enders <[email protected]>; [email protected] 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: [email protected] > > Firmensitz Köln > Amtsgericht Köln, HRB 73844 > > -----Ursprüngliche Nachricht----- > Von: Hans-Rudolf Hotz [mailto:[email protected]] > Gesendet: Dienstag, 17. Oktober 2017 10:33 > An: Matthias Enders <[email protected]>; > [email protected] > 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: [email protected] >> >> 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/
