* gnu/packages/bioinformatics.scm (preseq): Update to 2.0.
[source]: Add file-name field, remove patches.
[arguments]: Remove unused build phases, add make flags.
[inputs]: Add smithlab-cpp.
* gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch: Remove file.
* gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch: Remove
  file.
* gnu-system.am (dist_patch_DATA): Remove them.

* gnu/packages/bioinformatics.scm (smithlab-cpp): New variable.

* gnu/packages/bioinformatics.scm (edirect)[home-page]: Append trailing
  slash to home page.

* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.5.4.

* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.5.4.

* gnu/packages/bioinformatics.scm (ngs-java): Update to 1.2.2.
[arguments]: Remove build phase "fix-java-symlink-installation".

* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.2.

* gnu/packages/ruby.scm (ruby-net-ssh): New variable.

* gnu/packages/ruby.scm (ruby-mocha): New variable.

* gnu/packages/ruby.scm (ruby-redcarpet): New variable.

* gnu/packages/ruby.scm (ruby-introspection): New variable.

* gnu/packages/ruby.scm (ruby-instantiator): New variable.

* gnu/packages/ruby.scm (ruby-blankslate): New variable.

* gnu/packages/ruby.scm (ruby-metaclass): New variable.

* gnu/packages/ruby.scm (ruby-test-unit): New variable.

* gnu/packages/ruby.scm (ruby-packnga): New variable.

* gnu/packages/ruby.scm (ruby-gettext): New variable.

* gnu/packages/ruby.scm (ruby-text): New variable.

* gnu/packages/ruby.scm (ruby-locale): New variable.

* gnu/packages/ruby.scm (ruby-power-assert): New variable.

* gnu/packages/bioinformatics.scm (bless): Add supported-systems field.

* gnu/packages/bioinformatics.scm (htseq)[inputs]: Move python2-numpy
  from here ...
[propagated-inputs]: ... to here.

* gnu/packages/java.scm (ant): Update to 1.9.6.

* gnu/packages/package-management.scm (guix-devel): Update to 5c36edc8.

Suggested by Alex Vong <alexvong1995@gmail.com>.

* doc/guix.texi (Application Setup): Explain how to install X11 fonts
  for Asian languages.

* doc/guix.texi (operating-system Reference): The 'services' field now
  contains a list of service objects.

* gnu/packages/audio.scm (jack-2)[inputs]: Add python2-dbus.
[arguments]: Use python-2 and add build phase to wrap jack_control
Python script.

* gnu/services/base.scm (udev-rule): New procedure.
(kvm-udev-rule): Rewrite as variable in terms of udev-rule.

* gnu/packages/haskell.scm (ghc-unordered-containers)
  [arguments]: Remove.
  [inputs]: Add ghc-chasingbottoms, ghc-test-framework,
  ghc-test-framework-hunit, and ghc-test-framework-quickcheck2.

* gnu/packages/haskell.scm (ghc-chasingbottoms): New variable.

* gnu/packages/haskell.scm (ghc-attoparsec)[arguments]: Remove.
  [inputs]: Add ghc-quickcheck, ghc-quickcheck-unicode,
  ghc-test-framework, and ghc-test-framework-quickcheck2.

* gnu/packages/haskell.scm (ghc-test-framework-quickcheck2): New
  variable.

* gnu/packages/haskell.scm (ghc-async)[arguments]: Remove.
  [inputs]: Add ghc-hunit, ghc-test-framework, and
  ghc-test-framework-hunit.

* gnu/packages/haskell.scm (ghc-regex-posix): Propagate ghc-regex-base
  input.

* gnu/packages/haskell.scm (ghc-test-framework-hunit): New variable.

* gnu/packages/haskell.scm (ghc-test-framework): New variable.

* gnu/packages/haskell.scm (ghc-libxml): New variable.

* gnu/packages/haskell.scm (ghc-hostname): New variable.

* gnu/packages/terminals.scm (tilda): Update to 1.3.0.
[inputs]: Switch vte from 0.36 to 0.40, remove zip.

* gnu/packages/video.scm (youtube-dl): Update to 2015.11.18.