Re: galaxy-dev Digest, Vol 136, Issue 11

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Re: galaxy-dev Digest, Vol 136, Issue 11

M_Enders
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
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-----Ursprüngliche Nachricht-----
Von: galaxy-dev [mailto:[hidden email]] Im Auftrag von [hidden email]
Gesendet: Mittwoch, 18. Oktober 2017 18:00
An: [hidden email]
Betreff: galaxy-dev Digest, Vol 136, Issue 11
Priorität: Hoch

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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" <[hidden email]>
To: "[hidden email]"
        <[hidden email]>
Subject: [galaxy-dev] Problems with the test tool shed?
Message-ID: <[hidden email]>
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.


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Message: 2
Date: Tue, 17 Oct 2017 18:56:28 +0000
From: Martin Čech <[hidden email]>
To: "Von Kuster, Greg" <[hidden email]>,
        "[hidden email]"
        <[hidden email]>
Subject: Re: [galaxy-dev] Problems with the test tool shed?
Message-ID:
        <[hidden email]>
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 <[hidden email]> 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.
>
> ___________________________________________________________
> 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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> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/
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Message: 3
Date: Wed, 18 Oct 2017 08:56:17 +0200
From: Hans-Rudolf Hotz <[hidden email]>
To: Matthias Enders <[hidden email]>,
        "[hidden email]"
        <[hidden email]>
Subject: Re: [galaxy-dev] the future of trackster - was: galaxy-dev
        Digest, Vol 136, Issue 8
Message-ID: <[hidden email]>
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: [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/
>>>


------------------------------

Message: 4
Date: Wed, 18 Oct 2017 15:46:25 +0000
From: Deepak Tanwar <[hidden email]>
To: Galaxy Dev List <[hidden email]>
Subject: Re: [galaxy-dev] MACS2 Error
Message-ID:
        <[hidden email]>
       
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 <[hidden email]<mailto:[hidden email]>> 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

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Message: 5
Date: Wed, 18 Oct 2017 17:51:48 +0200
From: Devon Ryan <[hidden email]>
To: Deepak Tanwar <[hidden email]>, Galaxy Dev List
        <[hidden email]>
Subject: Re: [galaxy-dev] MACS2 Error
Message-ID: <[hidden email]>
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 <[hidden email]
>> <mailto:[hidden email]>> 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/
>
> To search Galaxy mailing lists use the unified search at:
>    http://galaxyproject.org/search/

--
Devon Ryan, PhD
Bioinformatician / Data manager
Bioinformatics Core Facility
Max Planck Institute for Immunobiology and Epigenetics
Email: [hidden email]

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Message: 6
Date: Wed, 18 Oct 2017 07:02:44 +0000
From: Enders Matthias <[hidden email]>
To: "[hidden email]"
        <[hidden email]>
Subject: [galaxy-dev] Problems with BlastDB.loc
Message-ID: <[hidden email]>
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
**********************************
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End of galaxy-dev Digest, Vol 136, Issue 11
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