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 galaxy-u...@bx.psu.edu 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 <scott.ti...@uvm.edu> 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:
pub...@nlm.nih.gov - for problems with PubMed
webad...@ncbi.nlm.nih.gov - 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]" <mat...@ncbi.nlm.nih.gov>:
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
mat...@ncbi.nlm.nih.gov
On 4/28/14 9:56 AM, "Scott W. Tighe" <scott.ti...@uvm.edu> 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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___________________________________________________________
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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--
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:
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