When will megablast be working again

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When will megablast be working again

Scott Tighe
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Re: [blast-help] When will megablast be working again

Matten, Wayne (NIH/NLM) [C]
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Re: [blast-help] When will megablast be working again

Scott Tighe
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Re: [blast-help] When will megablast be working again

Peter Cock
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Re: [blast-help] When will megablast be working again

Jen Hillman-Jackson
Hi Peter,

Thanks for clarifying all of this!

Main (usegalaxy.org) was restarted, perhaps why you encountered an
intermittent access delay. Let us know if are still unable to reach.

For the megablast issue over the weekend, we are updating the databases.
I replied to Scott's first [hidden email] post and also to a
similar question posted to Galaxy Biostar:
https://biostar.usegalaxy.org/p/7335/#7340

Take care,

Jen
Galaxy team

On 4/28/14 9:39 AM, Peter Cock wrote:

> Hi Scott,
>
> Could you clarify *which* Galaxy server you are using, and
> *which* megablast tool within Galaxy? Most BLAST options
> within Galaxy do NOT send the queries to the NCBI servers.
>
> (1) Main Public Galaxy
>
> I would guess you are using the main Galaxy Server, which
> only has this megablast wrapper using BLAST+ blastn
> internally for a limited set of databases (I would check but
> https://usegalaxy.org/ is down right now for me):
>
> galaxy-central/tools/metag_tools/megablast_wrapper.xml
>
> <tool id="megablast_wrapper" name="Megablast" version="1.2.0">
> ...
>
> Current Galaxy stable source link:
> https://bitbucket.org/galaxy/galaxy-dist/src/3b3365a391944f848b403412f226ee9e5499c0d5/tools/metag_tools/megablast_wrapper.xml?at=default
>
> (2) A local Galaxy with the BLAST+ wrappers
>
> The BLAST+ wrappers that I manage all run BLAST on the
> local server/cluster, although we are looking at an option
> to run this via the NCBI using the -remote switch:
> https://github.com/peterjc/galaxy_blast/issues/39
>
> (3) A local Galaxy with custom BLAST tools
>
> Are you perhaps using JJ's experimental BLAST+ wrappers
> with -remote support developed as part of the Galaxy-P project?
> See links on https://github.com/peterjc/galaxy_blast/issues/39
>
> Thanks,
>
> Peter
>
>
>
> On Mon, Apr 28, 2014 at 5:25 PM, Scott W. Tighe <[hidden email]> wrote:
>> Dear Wayne
>>
>> Here is the error message I get back.
>>
>> Server Error
>>
>> Your request could not be processed due to a problem on our Web server. This
>> could be a transient problem, please try the query again. If it doesn't
>> clear up within a reasonable period of time, e-mail a short description of
>> your query and the diagnostic information shown below to:
>>
>> [hidden email] - for problems with PubMed
>> [hidden email] - for problems with other services
>>
>> Thank you for your assistance. We will try to fix the problem as soon as
>> possible.
>>
>> Diagnostic Information:
>> Error: 500
>> URL: h t t p : / / b l a s t . n c b i . n l m . n i h . g o v / b l a s t /
>> B l a s t . c g i ?
>> Client: 130.14.26.12
>> Server: blast339
>> Time: Mon Apr 28 12:23:50 EDT 2014
>>
>> NOTE: The above is an internal URL which may differ from the one you used to
>> address the page.
>>
>> Rev. 01/04/08
>>
>>
>> --
>> Core Laboratory Research Staff
>> Advanced Genome Technologies Core
>> Deep Sequencing (MPS) Facility
>> Vermont Cancer Center
>> 149 Beaumont Ave
>> University of Vermont HSRF 303
>> Burlington Vermont  USA 05045
>> 802-656-AGTC
>> 802-999-6666 (cell)
>>
>>
>>
>> Quoting "Matten, Wayne (NIH/NLM) [C]" <[hidden email]>:
>>
>>> Hello, Scott,
>>>
>>> The web blast service, including megablast, is functioning normally. I
>>> don't know how Galaxy submits searches to us, but my guess is via our
>>> blast URLAPI, which is also functioning well at the moment.
>>>
>>> If your searches using our web page directly are also not working, please
>>> send me an RID from a search today, or describe a search in enough detail
>>> that I can reproduce it.
>>>
>>> Best regards,
>>> Wayne
>>>
>>> <<><<<><<<<<<>>>>>>>
>>> Wayne Matten, PhD
>>> NCBI Public Services
>>> [hidden email]
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 4/28/14 9:56 AM, "Scott W. Tighe" <[hidden email]> wrote:
>>>
>>>> Dear NCBI and Galaxy Team
>>>>
>>>> I have sent a note to determine when the Megablast option will be
>>>> active again. Whether you use Galaxy or NCBI directly, it is
>>>> inoperative.
>>>>
>>>> Scott
>>>>
>>>>
>>>> --
>>>> Core Laboratory Research Staff
>>>> Advanced Genome Technologies Core
>>>> Deep Sequencing (MPS) Facility
>>>> Vermont Cancer Center
>>>> 149 Beaumont Ave
>>>> University of Vermont HSRF 303
>>>> Burlington Vermont  USA 05045
>>>> 802-656-AGTC
>>>> 802-999-6666 (cell)
>>>>
>>>>
>>>>
>>>>
>>>>
>>
>>
>> ___________________________________________________________
>> The Galaxy User List is being replaced by the Galaxy Biostar
>> User Support Forum at https://biostar.usegalaxy.org/
>>
>> Posts to this list will be disabled in May 2014.  In the
>> meantime, you are encouraged to post all new questions to
>> Galaxy Biostar.
>>
>> For discussion of local Galaxy instances and the Galaxy
>> source code, please use the Galaxy Development list:
>>
>>   http://lists.bx.psu.edu/listinfo/galaxy-dev
>>
>> To manage your subscriptions to this and other Galaxy lists,
>> please use the interface at:
>>
>>   http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>>
>>   http://galaxyproject.org/search/mailinglists/
> ___________________________________________________________
> The Galaxy User List is being replaced by the Galaxy Biostar
> User Support Forum at https://biostar.usegalaxy.org/
>
> Posts to this list will be disabled in May 2014.  In the
> meantime, you are encouraged to post all new questions to
> Galaxy Biostar.
>
> For discussion of local Galaxy instances and the Galaxy
> source code, please use the Galaxy Development list:
>
>    http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
>    http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>
>    http://galaxyproject.org/search/mailinglists/

--
Jennifer Hillman-Jackson
http://galaxyproject.org

___________________________________________________________
The Galaxy User List is being replaced by the Galaxy Biostar
User Support Forum at https://biostar.usegalaxy.org/

Posts to this list will be disabled in May 2014.  In the
meantime, you are encouraged to post all new questions to
Galaxy Biostar.

For discussion of local Galaxy instances and the Galaxy
source code, please use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/
Jennifer Hillman-Jackson
http://galaxyproject.org
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Re: [blast-help] When will megablast be working again

Scott Tighe
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Re: [blast-help] When will megablast be working again

Peter Cock
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Re: [blast-help] When will megablast be working again

Scott Tighe
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