[EMBOSS] Compiling EMBOSS: missing jni.h?

Ryan Golhar golharam at umdnj.edu
Wed Nov 26 14:50:05 UTC 2008

You can obtain EMBOSS RPMs from http://informatics.umdnj.edu/BioRPMs

They compile cleanly and document dependencies.

charles-listes-emboss at plessy.org wrote:
> Le Tue, Nov 25, 2008 at 10:22:52AM -0500, Sylvain Foisy a écrit :
>> Thanks for the inputs on the paths toward java/javaos; make/make install now
>> worked...kind of. I need the Jemboss interface to facilitate my students'
>> interactions with EMBOSS, this is why I want to compile myself.
>> Now the "kind of" part: I hit a "libnucleus.so.6 not found" and it seems to
>> be related to the fact that libeplplot.so.3 is not found. I know that I have
>> the libplplot9/libplplot-dev packages installed. Any pointers? Could I use
>> your experimental package for emboss-libs to fix this?
> Hi Sylvain,
> EMBOSS uses a fork of libplplot, that was named libeplplot to allow both
> libraries to be installed on the same system. (By the way, is the fork still
> needed?) What seems to happen on your system is that it does not find the
> nucleus and eplplot libraries. Although it is not really recommended to mix
> local and packaged installs, the packages libajax6, libnucleus6 and emboss-lib
> may provide you what you need.
> I have started to implement support for jEMBOSS in the Debian packages, but it
> will take time before it reaches Debian archives. What you can do if you would
> like to try it is to unpack the emboss sources, and within them type
> "debcheckout emboss". Then you can use the protocol I gave you before, with
> mk-build-deps if still needed, and then debuild. On my amd64 system, I just
> checked that something would appear whan running runJemboss, but did not verify
> further that it functions correctly.
> Lastly, if all you need is an interface, you can try the emboss-explorer
> package, that provides a web frontend to EMBOSS.
> Have a nice day,

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