branch core-updates updated (ffddb42 -> 3a23036)

[Marius Bakke]

mbakke pushed a change to branch core-updates
in repository guix.

      from  ffddb42   Merge branch 'master' into core-updates
      adds  673364c   gnu: Add emacs-slime-repl-ansi-color.
      adds  9ab6c68   gnu: address@hidden: Update to 4.4.162.
      adds  c4a7a51   gnu: address@hidden: Update to 4.9.135.
      adds  668834c   gnu: address@hidden: Update to 4.14.78.
      adds  f7618bf   gnu: linux-libre: Update to 4.18.16.
      adds  9a6808e   gnu: tophat: Update to 2.1.1.
      adds  1d18ee6   gnu: bwa-pssm: Fetch from git.
      adds  2ba2d62   gnu: python2-bx-python: Update to 0.8.2.
      adds  f5cec00   gnu: Add python-bx-python.
      adds  8640f9e   gnu: python-twobitreader: Update to 3.1.6.
      adds  7321920   gnu: crossmap: Update to 0.2.9.
      adds  a5b0038   gnu: Add python-dnaio.
      adds  6b7260b   gnu: cutadapt: Update to 1.18.
      adds  6b31040   gnu: python-py2bit: Update to 0.3.0.
      adds  42643fc   gnu: python-dendropy: Fetch from git.
      adds  e6b65bd   gnu: eolie: Update to 0.9.45.
      adds  4d494a4   gnu: deeptools: Update to 3.1.3.
      adds  7a1e62c   gnu: delly: Update to 0.7.9.
      adds  1c06399   gnu: diamond: Fetch from git.
      adds  49b2e86   gnu: Add texlive-latex-doi.
      adds  893fbf1   gnu: Add texlive-generic-listofitems.
      adds  1d0669f   gnu: Add texlive-latex-readarray.
      adds  f50f343   gnu: Add texlive-latex-verbatimbox.
      adds  4348a05   gnu: Add texlive-latex-examplep.
      adds  5748fe5   gnu: discrover: Fetch from git.
      adds  949fa34   gnu: eigensoft: Update to 7.2.1.
      adds  c96ca68   gnu: edirect: Update to 10.2.20181018.
      adds  38622cc   gnu: express-beta-diversity: Update to 1.0.8.
      adds  0db75f7   gnu: fasttree: Use INVOKE.
      adds  50e33c3   gnu: python-screed: Update to 1.0.
      adds  4b8f453   gnu: khmer: Update to 2.1.2.
      adds  4d93a9a   gnu: seqan: Update to 2.4.0.
      adds  f8ee22f   gnu: flexbar: Update to 3.4.0.
      adds  aff38cb   install: Make /var/guix/…/guix-profile a relative symlink.
      adds  16d2125   gnu: Add python-ilinkedlist.
      adds  ff59835   gnu: light: Update to 1.2.
      adds  df71447   gnu: OpenSSH: Update to 7.9p1.
      adds  dc3dfa1   gnu: knot: Update to 2.7.3.
      adds  69c69c2   gnu: libmpdclient: Update to 2.16.
      adds  318ec0a   gnu: livemedia-utils: Update to 2018.10.17 [fixes 
CVE-2018-4013].
      adds  09aa3d0   gnu: Add r-ruvseq.
      adds  3a352a4   gnu: snap: Update to 4.2.2.2.
      adds  51f4e36   gnu: Add emacs-scribble-mode.
      adds  50401c2   gnu: libqtxdg: Update to 3.2.0.
      adds  9861bcd   gnu: liblxqt: Update to 0.13.0.
      adds  b456883   gnu: python-mistune: Update to 0.8.4.
      adds  f232c87   gnu: python-lazy-object-proxy: Update to 1.3.1.
      adds  3ad0a35   gnu: Add GN.
      adds  f38eedd   gnu: samba: Update to 4.8.6.
      adds  3743e11   gnu: libmd: Update to 1.0.1.
      adds  4350cac   gnu: xf86-input-libinput: Update to 0.28.1.
      adds  90fb136   gnu: xorg-server: Update to 1.20.2.
      adds  e810de3   gnu: python-m2crypto: python-typing is only needed for 
python2.
      adds  cb61baf   gnu: python-m2crypto: Update to 0.30.1.
      adds  1b50df7   gnu: python-markdown: Update home page.
      adds  9b9aaa5   gnu: python-markdown: Update to 3.0.1.
      adds  47d7c10   gnu: python-sure: Update to 1.4.11.
      adds  63abd1e   gnu: python-pymongo: Update to 3.7.2.
       new  c166a88   Merge branch 'master' into core-updates
       new  3a23036   gnu: python-datrie: Fix FTBFS with Python 3.7.

The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/build/install.scm                              |   2 +-
 gnu/local.mk                                       |   4 -
 gnu/packages/bioconductor.scm                      |  26 +
 gnu/packages/bioinformatics.scm                    | 658 +++++++++++----------
 gnu/packages/build-tools.scm                       |  58 ++
 gnu/packages/crypto.scm                            |   4 +-
 gnu/packages/dns.scm                               |   4 +-
 gnu/packages/education.scm                         |   8 +-
 gnu/packages/emacs.scm                             |  49 +-
 gnu/packages/gnome.scm                             |   6 +-
 gnu/packages/linux.scm                             |  46 +-
 gnu/packages/lxqt.scm                              |  72 ++-
 gnu/packages/mpd.scm                               |   4 +-
 .../patches/crossmap-allow-system-pysam.patch      | 121 ----
 .../patches/delly-use-system-libraries.patch       |  56 --
 gnu/packages/patches/liblxqt-include.patch         |  14 -
 .../patches/tophat-build-with-later-seqan.patch    |  24 -
 gnu/packages/python-crypto.scm                     |  12 +-
 gnu/packages/python.scm                            |  62 +-
 gnu/packages/samba.scm                             |   4 +-
 gnu/packages/ssh.scm                               |   4 +-
 gnu/packages/tex.scm                               | 189 ++++++
 gnu/packages/video.scm                             |   4 +-
 gnu/packages/xorg.scm                              |   8 +-
 24 files changed, 805 insertions(+), 634 deletions(-)
 delete mode 100644 gnu/packages/patches/crossmap-allow-system-pysam.patch
 delete mode 100644 gnu/packages/patches/delly-use-system-libraries.patch
 delete mode 100644 gnu/packages/patches/liblxqt-include.patch
 delete mode 100644 gnu/packages/patches/tophat-build-with-later-seqan.patch