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 -------------------------------------------------------- [email protected] [email protected] 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: [email protected] > [mailto:[email protected]] On Behalf Of Wolfgang Rumpf > Sent: Wednesday, March 16, 2011 10:11 AM > To: [email protected] > Cc: [email protected] > 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 > -------------------------------------------------------- > [email protected] > [email protected] > > Mobile - (614) 638-6797 > Skype - wolfgang.rumpf > > > > On Mar 16, 2011, at 5:25 AM, [email protected] 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. >> >> [email protected] 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 >>> -------------------------------------------------------- >>> [email protected] >>> [email protected] >>> >>> Mobile - (614) 638-6797 >>> Skype - wolfgang.rumpf >>> >>> >>> >>> >>> _______________________________________________ >>> EMBOSS mailing list >>> [email protected] >>> http://lists.open-bio.org/mailman/listinfo/emboss > > > _______________________________________________ > EMBOSS mailing list > [email protected] > http://lists.open-bio.org/mailman/listinfo/emboss > > _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
