Dear Galaxy-Dev List, the problem disappeared this day, as our IT was rebuilding the whole with galaxy-docker container. 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.enders@german-seed-alliance.de Firmensitz Köln Amtsgericht Köln, HRB 73844 -----Ursprüngliche Nachricht----- Von: galaxy-dev [mailto:galaxy-dev-bounces@lists.galaxyproject.org] Im Auftrag von galaxy-dev-request@lists.galaxyproject.org Gesendet: Mittwoch, 18. Oktober 2017 18:00 An: galaxy-dev@lists.galaxyproject.org Betreff: galaxy-dev Digest, Vol 136, Issue 11 Priorität: Hoch Send galaxy-dev mailing list submissions to galaxy-dev@lists.galaxyproject.org To subscribe or unsubscribe via the World Wide Web, visit https://lists.galaxyproject.org/listinfo/galaxy-dev or, via email, send a message with subject or body 'help' to galaxy-dev-request@lists.galaxyproject.org You can reach the person managing the list at galaxy-dev-owner@lists.galaxyproject.org When replying, please edit your Subject line so it is more specific than "Re: Contents of galaxy-dev digest..." HEY! This is important! If you reply to a thread in a digest, please 1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to. Why? 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. Today's Topics: 1. Problems with the test tool shed? (Von Kuster, Greg) 2. Re: Problems with the test tool shed? (Martin Čech) 3. Re: the future of trackster - was: galaxy-dev Digest, Vol 136, Issue 8 (Hans-Rudolf Hotz) 4. Re: MACS2 Error (Deepak Tanwar) 5. Re: MACS2 Error (Devon Ryan) 6. Problems with BlastDB.loc (Enders Matthias) ---------------------------------------------------------------------- Message: 1 Date: Tue, 17 Oct 2017 18:21:40 +0000 From: "Von Kuster, Greg" <ghv2@psu.edu> To: "galaxy-dev@lists.galaxyproject.org" <galaxy-dev@lists.galaxyproject.org> Subject: [galaxy-dev] Problems with the test tool shed? Message-ID: <9CCD9F8D-D91A-43AA-9F88-D7D777777AC9@mymail.psu.edu> Content-Type: text/plain; charset="utf-8" Hi all, I’m wondering if the TTS can be restarted. I’ve been seeing this of-and-on all afternoon. Thanks! Galaxy<http://galaxyproject.org/> The Test Tool Shed could not be reached You are seeing this message because a request to The Test Tool Shed timed out or was refused. This may be a temporary issue which could be resolved by retrying the operation you were performing. If you receive this message repeatedly or for an extended amount of time, please contact an administrator. -------------- next part -------------- An HTML attachment was scrubbed... URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20171017/1674d5c5/attachment-0001.html> ------------------------------ Message: 2 Date: Tue, 17 Oct 2017 18:56:28 +0000 From: Martin Čech <marten@bx.psu.edu> To: "Von Kuster, Greg" <ghv2@psu.edu>, "galaxy-dev@lists.galaxyproject.org" <galaxy-dev@lists.galaxyproject.org> Subject: Re: [galaxy-dev] Problems with the test tool shed? Message-ID: <CAHKBquHKS5zeCwc++8+BCvnqpRHtnowUTk0s62b9KTg6Et4iYQ@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Done, seems up now. Thanks for the report. M. On Tue, Oct 17, 2017 at 2:22 PM Von Kuster, Greg <ghv2@psu.edu> wrote:

Hi all,

I’m wondering if the TTS can be restarted. I’ve been seeing this of-and-on all afternoon.

Thanks!

Galaxy <http://galaxyproject.org/> The Test Tool Shed could not be reached

You are seeing this message because a request to The Test Tool Shed timed out or was refused. This may be a temporary issue which could be resolved by retrying the operation you were performing. If you receive this message repeatedly or for an extended amount of time, please contact an administrator.

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------------------------------ Message: 3 Date: Wed, 18 Oct 2017 08:56:17 +0200 From: Hans-Rudolf Hotz <hrh@fmi.ch> To: Matthias Enders <m.enders@german-seed-alliance.de>, "galaxy-dev@lists.galaxyproject.org" <galaxy-dev@lists.galaxyproject.org> Subject: Re: [galaxy-dev] the future of trackster - was: galaxy-dev Digest, Vol 136, Issue 8 Message-ID: <59E6FB11.4080900@fmi.ch> Content-Type: text/plain; charset="utf-8"; format=flowed 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: m.enders@german-seed-alliance.de

Firmensitz Köln Amtsgericht Köln, HRB 73844

-----Ursprüngliche Nachricht----- Von: Hans-Rudolf Hotz [mailto:hrh@fmi.ch] Gesendet: Dienstag, 17. Oktober 2017 16:50 An: Matthias Enders <m.enders@german-seed-alliance.de>; galaxy-dev@lists.galaxyproject.org 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: m.enders@german-seed-alliance.de

Firmensitz Köln Amtsgericht Köln, HRB 73844

-----Ursprüngliche Nachricht----- Von: Hans-Rudolf Hotz [mailto:hrh@fmi.ch] Gesendet: Dienstag, 17. Oktober 2017 10:33 An: Matthias Enders <m.enders@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.enders@german-seed-alliance.de

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/

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------------------------------ Message: 4 Date: Wed, 18 Oct 2017 15:46:25 +0000 From: Deepak Tanwar <dktanwar@hotmail.com> To: Galaxy Dev List <galaxy-dev@lists.galaxyproject.org> Subject: Re: [galaxy-dev] MACS2 Error Message-ID: <DM5PR0201MB3622F9AECC91FB13134EBB11DF4D0@DM5PR0201MB3622.namprd02.prod.outlook.com> Content-Type: text/plain; charset="utf-8" Hello, I am still facing problem. I have tried to reinstall MACS2 but nothing helped. Thank you! Deepak On Oct 16, 2017, at 4:00 PM, Deepak Tanwar <dktanwar@hotmail.com<mailto:dktanwar@hotmail.com>> wrote: Hi all, There is some problem with MACS2: export/galaxy-central/database/job_working_directory/000/380/tool_script.sh: line 25: macs2: command not found Fatal error: Exit code 127 () Tool installed: /shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2<http://toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2> Dependency Resolver Details Dependency Version Resolver Exact version Current Installation Status macs2 2.1.1.20160309 Conda True [http://192.168.99.100:32811/static/june_2007_style/blue/ok_small.png] gawk 4.1.3 Conda True [http://192.168.99.100:32811/static/june_2007_style/blue/ok_small.png] Thank you, Deepak -------------- next part -------------- An HTML attachment was scrubbed... URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20171018/15e250ef/attachment-0001.html> ------------------------------ Message: 5 Date: Wed, 18 Oct 2017 17:51:48 +0200 From: Devon Ryan <dpryan79@gmail.com> To: Deepak Tanwar <dktanwar@hotmail.com>, Galaxy Dev List <galaxy-dev@lists.galaxyproject.org> Subject: Re: [galaxy-dev] MACS2 Error Message-ID: <5592e574-694c-fe3a-ce13-5e340e73627e@gmail.com> Content-Type: text/plain; charset="windows-1252"; Format="flowed" Assuming you don't have galaxy set to clean up job working directories upon failure, have a look at the tool_script.sh in that directory and see if you can discern the issue. Also check the conda activation log file (under working/ I think) in that directory to see if it has anything useful. Devon On 10/18/2017 05:46 PM, Deepak Tanwar wrote:

Hello,

I am still facing problem. I have tried to reinstall MACS2 but nothing helped.

Thank you! Deepak

...

On Oct 16, 2017, at 4:00 PM, Deepak Tanwar <dktanwar@hotmail.com <mailto:dktanwar@hotmail.com>> wrote:

Hi all,

There is some problem with MACS2:

export/galaxy-central/database/job_working_directory/000/380/tool_script.sh: line 25: macs2: command not found Fatal error: Exit code 127 () Tool installed: /shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2 <http://toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2>

Dependency Resolver Details Dependency Version Resolver Exact version Current Installation Status macs2 2.1.1.20160309 Conda True gawk 4.1.3 Conda True

Thank you, Deepak

___________________________________________________________ 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/

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-- Devon Ryan, PhD Bioinformatician / Data manager Bioinformatics Core Facility Max Planck Institute for Immunobiology and Epigenetics Email: dpryan79@gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20171018/cd90cd16/attachment-0001.html> ------------------------------ Message: 6 Date: Wed, 18 Oct 2017 07:02:44 +0000 From: Enders Matthias <m.enders@npz-innovation.de> To: "galaxy-dev@lists.galaxyproject.org" <galaxy-dev@lists.galaxyproject.org> Subject: [galaxy-dev] Problems with BlastDB.loc Message-ID: <61B3F546DFD52B46B25883C23E2FF9DA294048BC@MAIL.npz.local> Content-Type: text/plain; charset="iso-8859-1" Dear Galaxy Dev List, we currently facing a problem with integrating new Blast Databases in our Galaxy instance. We added a the new DB to the file: /galaxy-central/tool-data/blastdb.loc But the new Database didn't show up in the respective tools, this situation remains also after restarting the galaxy instance and reloading the tool config (blasn for example). As we included several databases before (which worked fine) we tried to find the error an excluded (out-commented) an existing Db, but this database stayed in the tools. So the blastdb.loc file seems to be ignored by galaxy. (This is consistent for multiple users and browser, so we are sure this is not a client-sided Browser-Cache issue) So my questions are: Is there any kind of internal Cache in Galaxy which could explain this behavior? How can we track down / solve the issue? Our Galaxy Version is 17.05 Thanks a lot in advance! Mit freundlichen Grüßen i.A. Matthias Enders ********************************** [cid:image002.png@01CF9B54.EBA59810] NPZ Innovation GmbH Hohenlieth-Hof, D-24363 Holtsee Tel. +49-4351-736 189<tel:%2B49-4351-736%20189> Fax +49-4351-736 271<tel:%2B49-4351-736%20271> Mobil: +49-151-14247360<tel:%2B49-0151-14247360> Mail: m.enders@npz-innovation.de<mailto:m.enders@npz-innovation.de> Web: www.npz-innovation.de<http://www.npz-innovation.de/> Firmensitz Hohenlieth, Holtsee Amtsgericht Kiel, HRB 15342 Kl Geschäftsführer: Dr. Gunhild Leckband, Thorsten Pommer -------------- next part -------------- An HTML attachment was scrubbed... URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20171018/58cabcbb/attachment-0001.html> -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 6168 bytes Desc: image001.png URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20171018/58cabcbb/attachment-0001.png> ------------------------------ Subject: Digest Footer _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.galaxyproject.org https://lists.galaxyproject.org/listinfo/galaxy-dev To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ------------------------------ End of galaxy-dev Digest, Vol 136, Issue 11 *******************************************