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

[david.bauer at bayer.com]

Hi Wolfgang, 

mixing precompiled package installation with installations from source is 
dangerous and something one should never ever do.
In the normal emboss installation procedure (from source) you put the 
embassy packages within the source tree of emboss and run the compilation 
and installation from this place.
When I look at the directories you mention, where the emboss package is 
installed, this seems to be very ubuntu specific. So I hope someone who is 
familiar with ubuntu and/or the emboss package can help you with this.

David.

emboss-bounces at lists.open-bio.org schrieb am 16/03/2011 15:54:16:

> 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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> > http://lists.open-bio.org/mailman/listinfo/emboss
> > 
> > 
> 
> 
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