When will megablast be working again

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When will megablast be working again

Scott Tighe
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)





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

Matten, Wayne (NIH/NLM) [C]
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:

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

Scott Tighe
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)
>>
>>
>>
>>
>>



___________________________________________________________
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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

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please use the interface at:

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

Peter Cock
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:

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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:

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

Scott Tighe
In reply to this post by Peter Cock
Peter

Thank you for your detailed response and I should have noted that I was
using the Main Public Galaxy. Thank you for confirming that it is down!

I appreciate your input!

Scott

Scott Tighe
Senior Core Laboratory Research Staff
Advanced Genome Technologies Core
NextGen Sequencing/Flow Cytometry
University of Vermont and Vermont Cancer Center
149 Beaumont ave
Health Science Research Facility 303/305
Burlington Vermont 05405
802-656-2482 (AGTC)

On 4/28/2014 12:39 PM, 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:

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

Peter Cock
On Mon, Apr 28, 2014 at 9:01 PM, Scott Tighe <[hidden email]> wrote:
> Peter
>
> Thank you for your detailed response and I should have noted that I was
> using the Main Public Galaxy. Thank you for confirming that it is down!
>
> I appreciate your input!
>
> Scott

Hi Scott,

Galaxy is back for me now, and yes, the Galaxy tool you are
talking about is called Megablast (version 1.2.0), and only
offers these target databases:

htgs 13-Apr-2014
nt 17-Apr-2014
wgs 20-Apr-2014
phiX174

This Galaxy tool does *not* connect to the NCBI BLAST
service over the internet.

It sounds like the problem was due to the Galaxy team
updating these databases - as Jennifer mentioned?

I don't understand how you got an NCBI web server
error message (in your email to Wayne), but perhaps
you were separately testing the NCBI BLAST service
outside of Galaxy?

Regards,

Peter
___________________________________________________________
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:

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

Scott Tighe
Peter

Actually I was running blast separately and got error messages from them as well and I assumed it was a connection problem But in fact it was two separate problems unrelated. Good catch And thanks again

Scott
Vermont Cancer Center
Advanced Genome Techology Lab

On April 28, 2014 4:28:49 PM EDT, Peter Cock <[hidden email]> wrote:
On Mon, Apr 28, 2014 at 9:01 PM, Scott Tighe <[hidden email]> wrote:
Peter

Thank you for your detailed response and I should have noted that I was
using the Main Public Galaxy. Thank you for confirming that it is down!

I appreciate your input!

Scott

Hi Scott,

Galaxy is back for me now, and yes, the Galaxy tool you are
talking about is called Megablast (version 1.2.0), and only
offers these target databases:

htgs 13-Apr-2014
nt 17-Apr-2014
wgs 20-Apr-2014
phiX174

This Galaxy tool does *not* connect to the NCBI BLAST
service over the internet.

It sounds like the problem was due to the Galaxy team
updating these databases - as Jennifer mentioned?

I don't understand how you! got an NCBI web server
error message (in your email to Wayne), but perhaps
you were separately testing the NCBI BLAST service
outside of Galaxy?

Regards,

Peter

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