[BioBrew Users] Compiling with BioBrew EMBOSS

[Jeremy Mann]

I got the libs and devel package from the 4.1.2 BioBrew roll. The emnu
package at first I tried to use the configure script. Then I discover
the various errors as mentioned before. Then I started to edit the
Makefiles by hand, changing embdir and associated variables. It does
have an --enable-64 variable, but it doesn't want to link against the
shared libraries. So I went back to 32bit (-m32) and linked against
the static libs provided by BioBrew.

On 5/23/06, Glen Otero <glen at callident.com> wrote:
> Congratulations! That sounded very painful.
>
> Where did you get the libs and devel packages for EMBOSS? Did you
> install them and then build the emnu package by hand?
> How are you going to install emnu so that the user can access it?
> Just install it on the head node?
>
> Glen
>
> On May 23, 2006, at 10:01 AM, Jeremy Mann wrote:
>
> > Thanks for the reply Glen. I finally compiled it by hand in 32bit
> > mode with:
> >
> > gcc -m32 -O2 -o emnu emnu.o  -L/usr/lib -lmenu -lform -L/usr/X11R6/lib
> > -lX11 -lm -lncurses -Wl,--rpath -Wl,/usr/lib -Wl,--rpath -Wl,/usr/lib
> >
> > Its for this one researcher who wants to just type the menu (emnu) and
> > select his EMBOSS program.
> >
> > On 5/23/06, Glen Otero <glen at callident.com> wrote:
> >> Hmmm... this makes me think that there is a good reason why emnu
> >> isn't included in the EMBOSS package ; )
> >>
> >> Where did you get the devel and libs packages? Point me to them, and
> >> I can take a crack at building them.
> >> You might look for help about building these packages together on any
> >> EMBOSS lists that you can find .
> >> It looks like emnu has a not so clear relationship with EMBOSS and
> >> EMBASSY.
> >>
> >> Are you trying to build this for x86_64?
> >>
> >> Glen
> >>
> >> On May 23, 2006, at 8:31 AM, Jeremy Mann wrote:
> >>
> >> > I've installed the EMBOSS-libs and EMBOSS-devel packages and I'm
> >> > trying to compile EMNU against it. The problem is the configure
> >> script
> >> > runs embossversion and it inserts the InstallDirectory variable for
> >> > embprefix which is /var/tmp/EMBOSS-build. I can't seem to get
> >> around
> >> > this. I've tried to edit the two Makefiles for EMNU and I've tried
> >> > compiling it in 64 and 32 bit modes. The 64bit mode errors
> >> because it
> >> > can't link against the 32bit static libs and the 32bit mode errors
> >> > with:
> >> >
> >> > emnu.o(.text+0x1a58): In function `populate_program_menus':
> >> > : undefined reference to `ajListIterRead'
> >> > emnu.o(.text+0x1a63): In function `populate_program_menus':
> >> > : undefined reference to `ajListIterNext'
> >> > emnu.o(.text+0x1a76): In function `populate_program_menus':
> >> > : undefined reference to `ajStrLen'
> >> >
> >> > and on and on.
> >> >
> >> > Thanks for any help!
> >> >
> >> > --
> >> > Jeremy
> >> > _______________________________________________
> >> > BioBrew-Users mailing list
> >> > BioBrew-Users at bioinformatics.org
> >> > https://bioinformatics.org/mailman/listinfo/BioBrew-Users
> >> >
> >> >
> >>
> >> _______________________________________________
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> >>
> >
> >
> > --
> > Jeremy
> > _______________________________________________
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> > BioBrew-Users at bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/BioBrew-Users
> >
> >
>
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-- 
Jeremy