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Posted to users@taverna.apache.org by Marco Masseroli <ma...@polimi.it> on 2017/01/19 14:07:45 UTC
Re: Taverna Workbench Bioinformatics 2.5 - issue with local
service,"ncbi Gel Protein FASTA"
Hi Alan,
Do you have any news about the issue?
Thank you.
Best,
Marco
Il 05/01/2017 14.06, Marco Masseroli ha scritto:
> Hi Alan,
>
> Thank you for your fast answer.
> Please let me know when you have a possible solution.
>
> Best,
>
> Marco
>
>
> Il 05/01/2017 13.47, Alan Williams ha scritto:
>> On 05-Jan-17 11:54, Marco Masseroli wrote:
>>> Hi.
>>>
>>> Within the Taverna Workbench Bioinformatics 2.5, using the local
>>> service
>>> "ncbi Gel Protein FASTA" with input id "1220173" (as in the tutorial),
>>> now the returned result is:
>>>
>>> <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
>>> <html><head>
>>> <title>301 Moved Permanently</title>
>>> </head><body>
>>> <h1>Moved Permanently</h1>
>>> <p>The document has moved <a
>>> href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&db=protein&retmode=text&id=1220173">here</a>.</p>
>>>
>>> </body></html>
>>>
>>> I think all local services of "ncbi" included in the Workbench
>>> should be
>>> updated with the new url; could you please confirm (possibly adding
>>> when
>>> the update will be available)?
>>
>> Hello
>>
>> I can confirm the problem. It appears not to be as simple as changing
>> the script to fetch from https rather than http.
>>
>> I will discuss it with the other developers when they are back in the
>> New Year.
>>
>>> Thank you.
>>> Best,
>>>
>>> Marco
>>
>> Alan
>
--
*Marco Masseroli, PhD*
Associate Professor
Dipartimento di Elettronica, Informazione e Bioingegneria
Politecnico di Milano
Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
http://www.bioinformatics.deib.polimi.it/masseroli/
Tel. Office: +39 02 2399 3553; Lab: +39 02 2399 3631
Skype ID: masserolim
Re: Taverna Workbench Bioinformatics 2.5 - issue with local
service,"ncbi Gel Protein FASTA"
Posted by Alan Williams <al...@googlemail.com>.
Hello
Sorry for the long delay in replying.
I believe I have found a way round the issue. I'll describe it for
Windows. Let me know if you need it for Linux / MacOS.
(1) Go to the Taverna installation directory (where taverna.exe is) and
edit taverna.bat to delete the line that says:
set ARGS=%ARGS% "-Dcom.sun.net.ssl.enableECC=false"
(2) In the same directory edit taverna.vmoptions to delete the line that
says:
-Dcom.sun.net.ssl.enableECC=false
(3) In your workflow, you will have to change the local workers to use
https rather than http
They should now work.
Apologies again for the long delay. It was nasty to try to debug.
Alan