ADMIN.md

Gentoo Prefix - Admin guide

The research software repository is powered by Gentoo Prefix, which is essentially a full Gentoo distribution that is installed a directory of the host system.

This has the advantage that it does not require root privileges and can install newer software on an existing system without having to worry about backwards compatibility because it is installed on top of the host system.

The master branch tracks custom build scripts (ebuilds) and the ebi and yoda branches track configuration files. Custom build scripts should be pushed upstream to the Gentoo Science Project once they reach their quality standards. You can always send a pull request to that repository in order to have the admins review your approach.

Config files

• etc
  • bash
    • bashrc - default bashrc, LSF setup
  • portage
    • make.conf - global USE flags, make flags
    • package.provided - packages provided by host system
    • package.unmask - whitelisted masked packages
    • package.use - package-specific USE flags
    • package.accept_keywords - unstable keywords for otherwise stable system
  • vim
    • vimrc.local - default vim config
• usr
  • portage/profiles/prefix/linux
    • package.provided - list of packages provided by the host system
  • share/vim/vim74/colors
    • wombat.vim, wombat256.vim - wombat color scheme
• var
  • lib
    • layman
      • make.conf - configuration of overlays
    • portage
      • world - list of all explicitly installed packages

Using portage

Portage is Gentoo's package manager that will install and update packages, keep track of dependencies, and remove packages that are no longer needed.

The command-line tool is called emerge, and you can install packages by typing emerge <package name>.

Command-line arguments

Install a package with custom use flags (preferred: package.use file):

USE="flag1 -flag2" emerge something

Accept keywords (do not use this on global updates; preferred: package.accept_keywords file):

ACCEPT_KEYWORDS="**"

Overwrite system files:

FEATURES="-collision-detect -protect-owned" emerge =repo/pkg-version

Accept custom license:

ACCEPT_LICENSE="**" or "@FREE"

Using eselect

Selecting specific software versions

eselect python list      # lists all available python interpreters
eselect python set <num> # choose interpreter <num> as default

Read prefix-specific news

eselect news list        # list all items
eselect news read <num>  # read item with number <num>

Layman (overlay manager)

List available overlays:

layman -L

Add an overlay:

layman -a <overlay name>

Update all overlays:

layman -S

Packages are added to the main portage tree and can be installed and updated using emerge. Explicit referencing can be done with repo/pkg::overlay.

Manually building packages

All package files and patches are in usr/portage/*

To build a package manually, the commands are:

# edit the .ebuild file...
ebuild R-3.0.2.ebuild manifest
ebuild R-3.0.2.ebuild clean
ebuild R-3.0.2.ebuild configure # configure only
ebuild R-3.0.2.ebuild merge     # all steps, install after

The full list of options is below.

!!! clean      cleanrm    compile    config     configure  depend     
!!! digest     fetch      fetchall   help       info       install    
!!! manifest   merge      nofetch    package    postinst   postrm     
!!! preinst    prepare    prerm      pretend    qmerge     rpm        
!!! setup      test       unmerge    unpack