* gnu/packages/bioinformatics.scm (cufflinks): New variable.

* gnu/packages/bioinformatics.scm (tophat): New variable.
* gnu/packages/patches/tophat-build-with-later-seqan.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.

* gnu/packages/bioinformatics.scm (star): Update to 2.5.1b.
[source]: Remove bundled htslib sources and pre-built binaries.
[arguments]: Add phase "do-not-use-bundled-htslib".
[inputs]: Add "htslib".

* gnu/packages/bioinformatics.scm (star)[arguments]: Use "modify-phases"
  syntax.

* gnu/packages/linux.scm (fuse): Update to 2.9.5.

* gnu/packages/debug.scm (american-fuzzy-lop): Update to 1.96b.
  [arguments]: Create symbolic link to custom qemu, rather than copying.

Fixes regression introduced in 06da1a6b.

* gnu/packages/debug.scm (american-fuzzy-lop)[qemu]: Override inherited
  #:configure-flags.

* gnu/packages/admin.scm (iftop): New variable.

This reverts commit 45da8c6d.

* gnu/packages/admin.scm (iftop): New variable.

* tests/lint.scm: Add call to 'unsetenv' to remove 'http_proxy'.
* tests/publish.scm: Likewise.

* doc/guix.texi (Locales): Add missing 's'.

Fixes <http://bugs.gnu.org/22281>.
Reported by Christopher Allan Webber <cwebber@dustycloud.org>.

* gnu/system/grub.scm (eye-candy): Add 'root-fs' parameter.  Replace
'search --file' command in the output with whatever 'grub-root-search'
returns.
(grub-root-search): New procedure.
(grub-configuration-file): Add 'store-fs' parameter.  Use
'grub-root-search' instead of hard-coded 'search --file' commands.
* gnu/system.scm (store-file-system,
operating-system-store-file-system): New procedures.
(operating-system-grub.cfg): Use it, and adjust call to
'grub-configuration-file'.
* tests/system.scm: New file.
* Makefile.am (SCM_TESTS): Add it.

* gnu/packages/video.scm (ffmpeg): Update to 2.8.5.

* gnu/packages/messaging.scm (gajim): Update to 0.16.5.
  [arguments]: Disable tests.

* gnu/packages/dns.scm (bind-utils)[arguments]: Build and install
  "nsupdate" executable.

* gnu/packages/dns.scm (bind-utils)[arguments]: Generalize "build" and
  "install" phases.

* gnu/packages/dns.scm (bind-utils): Use "modify-phases" syntax.

* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.38-4.

* gnu/packages/audio.scm (libxmp): Update to 4.3.10.

* gnu/packages/lego.scm: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.

* guix/licenses.scm (mpl1.0): New variable.

* gnu/packages/bittorrent.scm (transmission-remote-cli): New variable.

Suggested by David Thompson <dthompson2@worcester.edu>
at <http://bugs.gnu.org/22402>.

* doc/guix.texi (Binary Installation): Explain how to make the Info
manual visible.

Suggested by <swedebugia@riseup.net>.

* doc/guix.texi (Using the Configuration System): Add
@unnumberedsubsubsec.  Explain how to remove services from a list.
Mention (gnu system).

* gnu/services/avahi.scm: Export 'avahi-service-type'.

* gnu/packages/admin.scm (isc-dhcp): Update bundled bind to 9.9.8-P3.

* gnu/packages/dns.scm (bind-utils): Update to 9.10.3-P3.

* gnu/packages/patches/linux-libre-CVE-2016-0728.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/linux.scm (linux-libre)[source]: Add patch.

* gnu/packages/video.scm (obs)[inputs]: Add v4l-utils.

* gnu/packages/video.scm (v4l-utils): New variable.

* gnu/packages/patches/arb-ldconfig.patch: Correct erroneously committed file.

This is a follow-up to commit ffc8f345.

* gnu/packages/algebra.scm (arb)[source]: Update to 2.8.1. Add patch.
* gnu/packages/patches/arb-ldconfig.patch: New file.
* gnu-system.am (dist_patch_DATA): Register patch.

Fixes <http://bugs.gnu.org/22391>.

* tests/cran.scm (beautify-description: use double spacing,
beautify-description: transform fragment into sentence). Move
from here ...
* tests/import-utils.scm: ... to here. New file.
* Makefile.am (SCM_TESTS): Add import-utils.

* guix/import/gem.scm (make-gem-sexp): Add synopsis argument.
(gem->guix-package): Pass unbeautified synopsis to make-gem-sexp.
* tests/gem.scm: Adapt it.

* guix/import/cran.scm (%bioconductor-updater,
latest-bioconductor-release, bioconductor-package?): New procedures.
(cran->guix-package): Support repositories other than CRAN.
(%bioconductor-url, %bioconductor-svn-url): New variables.
(description->package): Update signature to distinguish between packages
from different repositories.
(latest-release): Rename procedure ...
(latest-cran-release): ... to this.
(cran-package?): Do not assume all R packages are available on CRAN.
* tests/cran.scm: Update tests.
* guix/scripts/import/cran.scm: Add "--archive" option and default to
CRAN.
* guix/scripts/refresh.scm (%updaters): Add "%bioconductor-updater".
* doc/guix.texi: Document Bioconductor importer and updater.

* gnu/packages/enlightenment.scm (enlightenment): Update to 0.20.3.

* gnu/packages/xiph.scm (libshout): Update to 2.4.1.

* gnu/packages/xiph.scm (opusfile): Update to 0.7.

* gnu/packages/xiph.scm (opus): Update to 1.1.2.