Installing coot gtk2 build using overlays in Gentoo

About gentoo overlays

This excerpt is from the Gentoo users guide section about overlays  .  "Overlays" are package trees for Portage. They contain additional ebuilds for Gentoo. They are maintained by Gentoo developers, but are distributed separately from the main Portage tree. Donnie Berkholz has contributed several ebuilds of scientific software using his overlay. A list of overlays in the sci-chemistry and sci-biology sections are available by searching in this listing of portage overlays or in the lists below.

The overlays provided by Donnie BerkHolz have the following packages

1) dir /usr/portage/local/layman/dberkholz/sci-chemistry

sci-chemistry # ls
cclib   coot  epmr      kincontour  mopac2007-bin  prekin    pymol    theseus
ccp4    dssp  espresso  king        mopro-bin      procheck  pymss    tinker
ccp4mg  dsv   gamess    mage        pmb            profit    qutemol

2) dir  /usr/portage/local/layman/dberkholz/sci-biology

sci-biology # ls
biskit  foldx-bin  mmult  probalign  sap

3) dir /usr/portage/local/layman/dberkholz/sci-physics

sci-physics # ls
abinit  campos-asap  campos-ase  campos-dacapo  campos-gridpaw  exciting  octopus

 4) And importantly a whole listing of scientific libraries used extensively in crystallographic applicationstranscode sci-physics # dir /usr/portage/local dir /usr/portage/local/layman/dberkholz/sci-libs
ann  cctbx  mmtk  pgd-utils  pymmlib  vcg

Installing coot using the gentoo overlay

Follow these steps

1. emerge layman autounmask
2. layman -a dberkholz
3. autounmask sci-chemistry/coot-0.5*
4. emerge coot

Notes:

1) In some cases if ebuilds for the packages from the overlay fails. Try installing the ebuilds from the regular portage tree. Also if ccp4 compilation fails due to an error in syntax with  IDATE , make sure you are using the ~arch version of ccp4 ( echo sci-chemistry/ccp4 >> /etc/portage/package.keywords). Finally the svg icons on the coot side-bar seem to need the librsvg package . Not having this results in several warnings ( see below). This is easile fixed with an

emerge librsvg

** (coot-real:10601): WARNING **: Error loading pixmap file: /usr/share/coot/pix
maps/connect-to-ccp4.svg
** (coot-real:10601): WARNING **: Error loading pixmap file: /usr/share/coot/pix
maps/connect-to-oca.svg

These warnings go away after the emerge  librsvg.

2) The overlay uses a separate Fortran Eclass. If future ebuilds complain of  the eclass with a message like given below  , then comment out the line that sources the overlay make.conf in your master /etc/make.conf and then other ebuilds will progress normally

 #source /usr/portage/local/layman/make.conf

Error message seen with ebuilds if the make.conf from the overlay is sourced

* Overlay eclass overrides eclass from PORTDIR:
 *
 *   '/usr/portage/local/layman/dberkholz/eclass/fortran.eclass'
 *
 * It is best to avoid overridding eclasses from PORTDIR because it will
 * trigger invalidation of cached ebuild metadata that is distributed with
 * the portage tree. If you must override eclasses from PORTDIR then you
 * are advised to run `emerge --regen` after each time that you run `emerge
 * --sync`. Set PORTAGE_ECLASS_WARNING_ENABLE="0" in /etc/make.conf if you
 * would like to disable this warning.