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EMBOSS @ a59a6d4
boost @ 4cde250
libsequence-1.6.6 @ 362c259
staden_io_lib @ b08f55b


In contrib source packages are stored from other sources, which are
used (almost) unmodified by biolib, and which gracefully accept
patches sent upstream. This to allow some stability and, sometimes,
easier deployment.

When code is forked, and contains many changes, it moves to

For EMBOSS we import/update the CVS into git with (on Debian you need
the git-cvs package):

  cd ~/gitcvs

you don't want to do this directly in the biolib tree! And

  export CVSROOT=:pserver:cvs@cvs.open-bio.org:/home/repository/emboss
  cvs login # pwd cvs
  git cvsimport -v -d $CVSROOT -C EMBOSS emboss/emboss

or if you have a special branch (which you should have on update, to
make sure everything works):

  git cvsimport -o branch -v -d $CVSROOT -C EMBOSS emboss/emboss

If this all worked, and you are happy with the changes, synchronize
your biolib git submodule with this git repository.

After updating from CVS avoid changing the code a ./contrib tree - it
is a copy.

Note: this is up for reconsideration. Could well be we end up using
tarballs, as EMBOSS faithfully keeps all versions online.

For Bio++ a similar checkout is done:

  export CVSROOT=:pserver:anoncvs@kimura.univ-montp2.fr:/usr/local/cvsroot ; cvs login ; git cvsimport -v -d $CVSROOT -C numcalc numcalc