[EMBOSS] WG: Error in Emboss Explorer after updated EMBOSS to 6.5.7

[David Bauer]

Hi Wolfgang,

this issue already appeared some time ago.
It seems that the emboss explorer at sourceforge is no longer maintained.
I did a quick fix to the modules so that they work again with the latest EMBOSS release.
Please try it out and drop me a note if it works for you.

Kind regards,
David.


-----Ursprüngliche Nachricht-----
Von: David Bauer 
Gesendet: 26 October 2012 10:10
An: 'Jean Mao'
Betreff: AW: [EMBOSS] Error in Emboss Explorer after updated EMBOSS to 6.5.7

Hi Jean,

I found the real reason for this problem and fixed it in the XHTML.pm module.
There are also some minor additions for the ontology lookup programs.
If your system is running, you can just replace the old modules with the new ones in the attached tar file.
On my system those modules are installed in "/usr/local/lib/perl5/site_perl/5.14.2/EMBOSS".

Kind regards,
David.

-----Ursprüngliche Nachricht-----
Von: Jean Mao [mailto:maoj at mail.nih.gov] 
Gesendet: 24 October 2012 13:46
An: David Bauer
Betreff: Re: AW: AW: [EMBOSS] Error in Emboss Explorer after updated EMBOSS to 6.5.7

Hi David,

Thank you so much for looking into this. I will try it and let you know.

Regards,

Jean

On 10/24/12 07:16, David Bauer wrote:
> Hi Jean,
>
> sorry for coming back to you so late but I had some other things on my schedule with higher priority....
>
> The problem is the extractalign program in the group ALIGN.
> I do not yet fully understand what is exactly the problem but this is the only program in the top level ALIGN group which itself has several subgroups "ALIGN LOCAL" etc. This structure is new and unique and somehow this situation confuses the parser.
>
> So there are 2 quick fixes (or better workarounds) possible:
>
> 1) change the extractalign.acd file
> If you just change this from
> groups: "Alignment, Data retrieval:Sequence data, Edit"
> to
> groups: "Data retrieval:Sequence data, Edit"
> and the emboss explorer works again as expected :-)
>
> 2) exclude the ALIGN group from the emboss explorer menu
> In Conf.pm there is an @EXCLUDED variable which can be used to exclude individual programs or groups from the interface.
> You can simply add "ALIGNMENT" to this.
> It will only remove the ALIGNEMENT group from the display.
> Because extractalign is also in the groups EDIT and DATA RETRIEVAL SEQUENCE DATA, the program will still be there but just not listed under the ALIGNMENT group.
>
>
> I will try to find a better fix for this problem and also add the new data types for the ontology apps.
>
>
> Kind regards,
> David.
>
>
> -----Ursprüngliche Nachricht-----
> Von: Jean Mao [mailto:maoj at mail.nih.gov]
> Gesendet: 05 September 2012 13:29
> An: David Bauer
> Betreff: Re: AW: [EMBOSS] Error in Emboss Explorer after updated EMBOSS to 6.5.7
>
> Hi David,
>
> Thank you very much for getting back to me. I also really appreciate
> that you are willing to spend your time to check into this.
>
> Regards,
>
> Jean
>
> On 09/05/12 02:46, David Bauer wrote:
>> Hi Jean,
>>
>> I've been using the emboss explorer in the past, when I was responsible for providing this package to our users.
>> Since my focus has shifted, I use emboss just for my own work, where I don't need the web interface.
>>
>> The emboss explorer interface is created dynamically from the acd files and there have been several fundamental changes in the last few emboss versions to those.
>>
>> I will take a look at this to see, if I can get the emboss explorer working again with the latest emboss version.
>>
>>
>> Kind regards,
>> David.
>>
>> -----Urspr�ngliche Nachricht-----
>> Von: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] Im Auftrag von Jean Mao
>> Gesendet: 04 September 2012 17:31
>> An: emboss at lists.open-bio.org
>> Betreff: [EMBOSS] Error in Emboss Explorer after updated EMBOSS to 6.5.7
>>
>> Hi,
>>
>> I know this list is for EMBOSS, not emboss explorer. However, I am not
>> sure where to look for help with emboss explorer anymore so I am trying
>> my luck here. Really appreciate if someone can point me to the right
>> direction.
>>
>> Recently I updated emboss to 6.5.7 from 6.3.1. Emboss Explorer was
>> functional before I switched the link. Once the link is switched to
>> point to 6.5.7, the main manu panel on the left of the webpage is
>> comletely messed up. In stead of showing categories and apps under each
>> category, now there is only categories showing and no apps that one can
>> click and load. The most current emboss explorer I can find is 2.2.0 and
>> was out since 2006.
>>
>> Regards,
>>
>> Jean
>>
>> _______________________________________________
>> EMBOSS mailing list
>> EMBOSS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/emboss
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