[EMBOSS] Antwort: Vienna in Emboss/Emboss-Explorer on Ubuntu?

[Wolfgang Rumpf]

I most certainly am HOPING to use the embassy package - that's the one I downloaded.  Again, is there any special command I need to use during the ./configure process in order to ensure that it goes into the correct locations (those corresponding to the locations where Emboss/Embassy were installed by the precompiled binaries from the Ubuntu Software Center)?  To clarify - I did NOT compile emboss/embassy myself; the Ubuntu Software Center installed those for me.  But now I want to add Vienna, and must do so by compiling, and I want it to "seamlessly" work with my existing Emboss/Embassy install....


Wolfgang

Dr. Wolfgang Rumpf
Product Specialist, Rescentris Inc.
Adjunct Faculty, Dept. of Biotechnology, UMUC
--------------------------------------------------------
wolfgang.rumpf at rescentris.com
wolfgang.rumpf at gmail.com

Mobile - (614) 638-6797
Skype - wolfgang.rumpf



On Mar 16, 2011, at 10:50 AM, Lapointe, David wrote:

> Are you using the embassy package for ViennaRNA? That compiles along with EMBOSS and ends up quite nicely with emboss-explorer. Use the software from here ftp://emboss.open-bio.org/pub/EMBOSS/  so the acd files are created.
> 
> David
> 
> --
> David Lapointe, Ph.D.
> Director Scientific Computing/Information Services
> University of Massachusetts Medical School
> 55 Lake Avenue N
> Worcester MA 01655
> 508-856-5141 (v)
> 
> 
> 
> -----Original Message-----
> From: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of Wolfgang Rumpf
> Sent: Wednesday, March 16, 2011 10:11 AM
> To: david.bauer at bayer.com
> Cc: emboss at lists.open-bio.org
> Subject: Re: [EMBOSS] Antwort: Vienna in Emboss/Emboss-Explorer on Ubuntu?
> 
> David, I suspected as much - I think my real concern is that I don't necessarily know the proper command-line syntax to control where the installation occurs.  My EMBOSS proper is in /usr/lib/emboss/; there appear to be additional files in /usr/share/emboss (e.g. acd, data, doc) and in /usr/share/emboss-explorer.  These should be the default locations for the packages from the Software Center in Ubuntu.
> 
> So given that, when I configure Vienna, do I tell Vienna that it will live in /usr/share/emboss by typing  ./configure --prefix=/usr/lib/emboss - or is there something I'm missing?
> 
> 
> Wolfgang
> 
> Dr. Wolfgang Rumpf
> Product Specialist, Rescentris Inc.
> Adjunct Faculty, Dept. of Biotechnology, UMUC
> --------------------------------------------------------
> wolfgang.rumpf at rescentris.com
> wolfgang.rumpf at gmail.com
> 
> Mobile - (614) 638-6797
> Skype - wolfgang.rumpf
> 
> 
> 
> On Mar 16, 2011, at 5:25 AM, david.bauer at bayer.com wrote:
> 
>> 
>> Hi, 
>> 
>> the emboss-explorer creates the html menu on the fly by calling the emboss program wossname. 
>> So if you install the Vienna embassy package just in the same place like the main emboss, the vrnafold etc. should appear in the emboss-explorer. 
>> But I'm not using it on Ubuntu so I do not know if there are any Ubuntu specific issues. 
>> 
>> HTH, 
>> David. 
>> 
>> emboss-bounces at lists.open-bio.org schrieb am 15/03/2011 21:49:47:
>> 
>>> One of the ideas I try to teach in my bioinformatics class is RNA 
>>> folding - and as such I'd love to add an RNA folding algorithm to my
>>> bioinformatics server.  It seems like the "easiest" path might be 
>>> Vienna since there's an EMBOSS port of it.  I'm not sure how to 
>>> proceed, however - I've downloaded the source (VIENNA-1.7.2) and 
>>> know the rough procedure for getting it installed, but I want it to 
>>> "hook in" to my existing Ubuntu EMBOSS-Explorer (which is how my 
>>> students access all of the other analyses we do).  Any ideas how to 
>>> modify the installation to install to the correct path so that it 
>>> will be available in my existing applications list?
>>> 
>>> Any help appreciated - thanks in advance!
>>> 
>>> 
>>> Wolfgang
>>> 
>>> Dr. Wolfgang Rumpf
>>> Product Specialist, Rescentris Inc.
>>> Adjunct Faculty, Dept. of Biotechnology, UMUC
>>> --------------------------------------------------------
>>> wolfgang.rumpf at rescentris.com
>>> wolfgang.rumpf at gmail.com
>>> 
>>> Mobile - (614) 638-6797
>>> Skype - wolfgang.rumpf
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> EMBOSS mailing list
>>> EMBOSS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/emboss
> 
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