diff --git a/gnu/build/install.scm b/gnu/build/install.scm
index 5a5e703872..c602d69489 100644
--- a/gnu/build/install.scm
+++ b/gnu/build/install.scm
@@ -199,7 +199,7 @@ (define (symlink* old new)
   (mkdir-p* %root-profile)
   (symlink* profile
             (string-append %root-profile "/guix-profile-1-link"))
-  (symlink* (string-append %root-profile "/guix-profile-1-link")
+  (symlink* "guix-profile-1-link"
             (string-append %root-profile "/guix-profile"))
 
   (mkdir-p* "/root")
diff --git a/gnu/local.mk b/gnu/local.mk
index befe3c4b33..e0bd43164c 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -635,7 +635,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/cracklib-fix-buffer-overflow.patch	\
   %D%/packages/patches/crawl-upgrade-saves.patch		\
   %D%/packages/patches/crda-optional-gcrypt.patch		\
-  %D%/packages/patches/crossmap-allow-system-pysam.patch	\
   %D%/packages/patches/clucene-contribs-lib.patch               \
   %D%/packages/patches/cube-nocheck.patch			\
   %D%/packages/patches/cursynth-wave-rand.patch			\
@@ -644,7 +643,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/datamash-arm-tests.patch			\
   %D%/packages/patches/dbus-helper-search-path.patch		\
   %D%/packages/patches/deja-dup-use-ref-keyword-for-iter.patch	\
-  %D%/packages/patches/delly-use-system-libraries.patch		\
   %D%/packages/patches/dfu-programmer-fix-libusb.patch		\
   %D%/packages/patches/diffutils-gets-undeclared.patch		\
   %D%/packages/patches/diffutils-getopt.patch			\
@@ -890,7 +888,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/libjxr-fix-function-signature.patch	\
   %D%/packages/patches/libjxr-fix-typos.patch			\
   %D%/packages/patches/libotr-test-auth-fix.patch		\
-  %D%/packages/patches/liblxqt-include.patch			\
   %D%/packages/patches/libmad-armv7-thumb-pt1.patch		\
   %D%/packages/patches/libmad-armv7-thumb-pt2.patch		\
   %D%/packages/patches/libmad-frame-length.patch		\
@@ -1180,7 +1177,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/tk-find-library.patch			\
   %D%/packages/patches/ttf2eot-cstddef.patch			\
   %D%/packages/patches/ttfautohint-source-date-epoch.patch	\
-  %D%/packages/patches/tophat-build-with-later-seqan.patch	\
   %D%/packages/patches/totem-meson-easy-codec.patch		\
   %D%/packages/patches/tuxpaint-stamps-path.patch		\
   %D%/packages/patches/twinkle-include-qregexpvalidator.patch	\
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1b779855b2..92b67453f6 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -913,3 +913,29 @@ (define-public r-dnabarcodes
 barcodes.  Finally, reads that start with a (possibly mutated) barcode can be
 demultiplexed, i.e. assigned to their original reference barcode.")
     (license license:gpl2)))
+
+(define-public r-ruvseq
+  (package
+    (name "r-ruvseq")
+    (version "1.14.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "RUVSeq" version))
+       (sha256
+        (base32
+         "16i5sm5af761k4zvspfi8jknsgln48bn538hxqqmlaq7wvlfxqxj"))))
+    (properties `((upstream-name . "RUVSeq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-edaseq" ,r-edaseq)
+       ("r-edger" ,r-edger)
+       ("r-mass" ,r-mass)))
+    (home-page "https://github.com/drisso/RUVSeq")
+    (synopsis "Remove unwanted variation from RNA-Seq data")
+    (description
+     "This package implements methods to @dfn{remove unwanted variation} (RUV)
+of Risso et al. (2014) for the normalization of RNA-Seq read counts between
+samples.")
+    (license license:artistic2.0)))
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1e04081ceb..96ea07bdc4 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1332,7 +1332,7 @@ (define-public bowtie
 (define-public tophat
   (package
     (name "tophat")
-    (version "2.1.0")
+    (version "2.1.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1340,13 +1340,12 @@ (define-public tophat
                     version ".tar.gz"))
               (sha256
                (base32
-                "168zlzykq622zbgkh90a90f1bdgsxkscq2zxzbj8brq80hbjpyp7"))
-              (patches (search-patches "tophat-build-with-later-seqan.patch"))
+                "19add02kv2xhd6ihd779dr7x35ggym3jqr0m5c4315i1yfb0p11p"))
               (modules '((guix build utils)))
               (snippet
                '(begin
                   ;; Remove bundled SeqAn and samtools
-                  (delete-file-recursively "src/SeqAn-1.3")
+                  (delete-file-recursively "src/SeqAn-1.4.2")
                   (delete-file-recursively "src/samtools-0.1.18")
                   #t))))
     (build-system gnu-build-system)
@@ -1383,7 +1382,7 @@ (define-public tophat
        ("python" ,python-2)
        ("perl" ,perl)
        ("zlib" ,zlib)
-       ("seqan" ,seqan)))
+       ("seqan" ,seqan-1)))
     (home-page "http://ccb.jhu.edu/software/tophat/index.shtml")
     (synopsis "Spliced read mapper for RNA-Seq data")
     (description
@@ -1450,13 +1449,14 @@ (define-public bwa-pssm
     (name "bwa-pssm")
     (version "0.5.11")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/pkerpedjiev/bwa-pssm/"
-                                  "archive/" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/pkerpedjiev/bwa-pssm.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "02p7mpbs4mlxmn84g2x4ghak638vbj4lqix2ipx5g84pz9bhdavg"))))
+                "076c4q0cdqz8jgylb067y9zmvxglppnzi3qiscn0xiypgc6lgb5r"))))
     (build-system gnu-build-system)
     (inputs
      `(("gdsl" ,gdsl)
@@ -1474,40 +1474,38 @@ (define-public bwa-pssm
 well as many of the command line options.")
     (license license:gpl3+)))
 
-(define-public python2-bx-python
+(define-public python-bx-python
   (package
-    (name "python2-bx-python")
-    (version "0.7.3")
+    (name "python-bx-python")
+    (version "0.8.2")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "bx-python" version))
               (sha256
                (base32
-                "15z2w3bvnc0n4qmb9bd6d8ylc2h2nj883x2w9iixf4x3vki9b22i"))
-              (modules '((guix build utils)))
-              (snippet
-               '(begin
-                  (substitute* "setup.py"
-                    ;; remove dependency on outdated "distribute" module
-                    (("^from distribute_setup import use_setuptools") "")
-                    (("^use_setuptools\\(\\)") ""))
-                  #t))))
+                "11kksg2rbzihpmcid823xvg42xi88m7sz58rzk29abybkxy0rszs"))))
     (build-system python-build-system)
-    (arguments
-     `(#:tests? #f ;tests fail because test data are not included
-       #:python ,python-2))
+    ;; Tests fail because test data are not included
+    (arguments '(#:tests? #f))
+    (propagated-inputs
+     `(("python-numpy" ,python-numpy)
+       ("python-six" ,python-six)))
     (inputs
-     `(("python-numpy" ,python2-numpy)
-       ("zlib" ,zlib)))
+     `(("zlib" ,zlib)))
     (native-inputs
-     `(("python-nose" ,python2-nose)))
-    (home-page "http://bitbucket.org/james_taylor/bx-python/")
+     `(("python-lzo" ,python-lzo)
+       ("python-nose" ,python-nose)
+       ("python-cython" ,python-cython)))
+    (home-page "https://github.com/bxlab/bx-python")
     (synopsis "Tools for manipulating biological data")
     (description
      "bx-python provides tools for manipulating biological data, particularly
 multiple sequence alignments.")
     (license license:expat)))
 
+(define-public python2-bx-python
+  (package-with-python2 python-bx-python))
+
 (define-public python-pysam
   (package
     (name "python-pysam")
@@ -1597,19 +1595,19 @@ (define-public python2-pysam
 (define-public python-twobitreader
   (package
     (name "python-twobitreader")
-    (version "3.1.4")
+    (version "3.1.6")
     (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "twobitreader" version))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/benjschiller/twobitreader")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1q8wnj2kga9nz1lwc4w7qv52smfm536hp6mc8w6s53lhyj0mpi22"))))
+                "1qbxvv1h58cismbk1anpjrkpghsaiy64a11ir3lhy6qch6xf8n62"))))
     (build-system python-build-system)
-    (arguments
-     '(;; Tests are not distributed in the PyPi release.
-       ;; TODO Try building from the Git repo or asking the upstream maintainer
-       ;; to distribute the tests on PyPi.
-       #:tests? #f))
+    ;; Tests are not included
+    (arguments '(#:tests? #f))
     (native-inputs
      `(("python-sphinx" ,python-sphinx)))
     (home-page "https://github.com/benjschiller/twobitreader")
@@ -1896,31 +1894,18 @@ (define-public clustal-omega
 (define-public crossmap
   (package
     (name "crossmap")
-    (version "0.2.1")
+    (version "0.2.9")
     (source (origin
               (method url-fetch)
-              (uri (string-append "mirror://sourceforge/crossmap/CrossMap-"
-                                  version ".tar.gz"))
+              (uri (pypi-uri "CrossMap" version))
               (sha256
                (base32
-                "07y179f63d7qnzdvkqcziwk9bs3k4zhp81q392fp1hwszjdvy22f"))
-              ;; This patch has been sent upstream already and is available
-              ;; for download from Sourceforge, but it has not been merged.
-              (patches (search-patches "crossmap-allow-system-pysam.patch"))
-              (modules '((guix build utils)))
-              (snippet '(begin
-                          ;; remove bundled copy of pysam
-                          (delete-file-recursively "lib/pysam")
-                          #t))))
+                "1byhclrqnqpvc1rqkfh4jwj6yhn0x9y7jk47i0qcjlhk0pjkw92p"))))
     (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'set-env
-           (lambda _ (setenv "CROSSMAP_USE_SYSTEM_PYSAM" "1") #t)))))
+    (arguments `(#:python ,python-2))
     (inputs
-     `(("python-numpy" ,python2-numpy)
+     `(("python-bx-python" ,python2-bx-python)
+       ("python-numpy" ,python2-numpy)
        ("python-pysam" ,python2-pysam)
        ("zlib" ,zlib)))
     (native-inputs
@@ -1934,22 +1919,46 @@ (define-public crossmap
 file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
     (license license:gpl2+)))
 
+(define-public python-dnaio
+  (package
+    (name "python-dnaio")
+    (version "0.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "dnaio" version))
+       (sha256
+        (base32
+         "0f16m7hdlm0fz1n7y5asy0v9ghyrq17ni1p9iybq22ddzyd49r27"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("python-cython" ,python-cython)
+       ("python-pytest" ,python-pytest)
+       ("python-xopen" ,python-xopen)))
+    (home-page "https://github.com/marcelm/dnaio/")
+    (synopsis "Read FASTA and FASTQ files efficiently")
+    (description
+     "dnaio is a Python library for fast parsing of FASTQ and also FASTA
+files.  The code was previously part of the cutadapt tool.")
+    (license license:expat)))
+
 (define-public cutadapt
   (package
     (name "cutadapt")
-    (version "1.16")
+    (version "1.18")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/marcelm/cutadapt.git")
                     (commit (string-append "v" version))))
-              (file-name (string-append name "-" version "-checkout"))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "09pr02067jiks19nc0aby4xp70hhgvb554i2y1c04rv1m401w7q8"))))
+                "08bbfwyc0kvcd95jf2s95xiv9s3cbsxm39ydl0qck3fw3cviwxpg"))))
     (build-system python-build-system)
     (inputs
-     `(("python-xopen" ,python-xopen)))
+     `(("python-dnaio" ,python-dnaio)
+       ("python-xopen" ,python-xopen)))
     (native-inputs
      `(("python-cython" ,python-cython)
        ("python-pytest" ,python-pytest)))
@@ -2044,15 +2053,15 @@ (define-public python-dendropy
     (version "4.4.0")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
        ;; Source from GitHub so that tests are included.
-       (uri
-        (string-append "https://github.com/jeetsukumaran/DendroPy/archive/v"
-                       version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (uri (git-reference
+             (url "https://github.com/jeetsukumaran/DendroPy.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "0v2fccny5xjaah546bsch1mw4kh61qq5frz2ibllxs9mp6ih9bsn"))))
+         "097hfyv2kaf4x92i4rjx0paw2cncxap48qivv8zxng4z7nhid0x9"))))
     (build-system python-build-system)
     (home-page "http://packages.python.org/DendroPy/")
     (synopsis "Library for phylogenetics and phylogenetic computing")
@@ -2082,14 +2091,14 @@ (define-public python2-dendropy
 (define-public python-py2bit
   (package
     (name "python-py2bit")
-    (version "0.2.1")
+    (version "0.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "py2bit" version))
        (sha256
         (base32
-         "1cdf4qlmgwsh1f4k0wdv2sr8x9qn4366p0k3614vbd0fpqiarxrl"))))
+         "1vw2nvw1yrl7ikkqsqs1pg239yr5nspvd969r1x9arms1k25a1a5"))))
     (build-system python-build-system)
     (home-page "https://github.com/dpryan79/py2bit")
     (synopsis "Access 2bit files using lib2bit")
@@ -2101,7 +2110,7 @@ (define-public python-py2bit
 (define-public deeptools
   (package
     (name "deeptools")
-    (version "3.1.2")
+    (version "3.1.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -2110,7 +2119,7 @@ (define-public deeptools
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "06fdpp6cg3xiwryxjhixvfysl4z0ps1crjgia587qa9ikqpsa7fd"))))
+                "1vggnf52g6q2vifdl4cyi7s2fnfqq0ky2zrkj5zv2qfzsc3p3siw"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -2146,42 +2155,42 @@ (define-public deeptools
 (define-public delly
   (package
     (name "delly")
-    (version "0.7.7")
+    (version "0.7.9")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/tobiasrausch/delly/archive/v"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/dellytools/delly.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
-               (base32 "0dkwy3pyxmi6dhh1lpsr3698ri5sslw9qz67hfys0bz8dgrqwabj"))
-              (patches (search-patches "delly-use-system-libraries.patch"))))
+               (base32 "034jqsxswy9gqdh2zkgc1js99qkv75ks4xvzgmh0284sraagv61z"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  (delete-file-recursively "src/htslib")
+                  #t))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; There are no tests to run.
-       #:make-flags '("PARALLEL=1") ; Allow parallel execution at run-time.
+       #:make-flags
+       (list "PARALLEL=1"  ; Allow parallel execution at run-time.
+             (string-append "prefix=" (assoc-ref %outputs "out")))
        #:phases
        (modify-phases %standard-phases
          (delete 'configure) ; There is no configure phase.
-         (replace 'install
-           (lambda _
-             (let ((bin (string-append (assoc-ref %outputs "out") "/bin"))
-                   (templates (string-append (assoc-ref %outputs "out")
+         (add-after 'install 'install-templates
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((templates (string-append (assoc-ref outputs "out")
                                              "/share/delly/templates")))
-               (mkdir-p bin)
                (mkdir-p templates)
                (copy-recursively "excludeTemplates" templates)
-               (install-file "src/cov" bin)
-               (install-file "src/delly" bin)
-               (install-file "src/dpe" bin)))))))
-    (native-inputs
-     `(("python" ,python-2)))
+               #t))))))
     (inputs
      `(("boost" ,boost)
        ("htslib" ,htslib)
        ("zlib" ,zlib)
        ("bzip2" ,bzip2)))
-    (home-page "https://github.com/tobiasrausch/delly")
+    (home-page "https://github.com/dellytools/delly")
     (synopsis "Integrated structural variant prediction method")
     (description "Delly is an integrated structural variant prediction method
 that can discover and genotype deletions, tandem duplications, inversions and
@@ -2195,14 +2204,14 @@ (define-public diamond
     (name "diamond")
     (version "0.9.22")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/bbuchfink/diamond/archive/v"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/bbuchfink/diamond.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0adp87r9ak63frdrdmrdfhsn6g0jnnyq1lr2wibvqbxcl37iir9m"))))
+                "0bky78v79g3wmdpsd706cscckgw1v09fg8vdd0z8z0d5b97aj9zl"))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f ; no "check" target
@@ -2230,13 +2239,14 @@ (define-public discrover
     (version "1.6.0")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/maaskola/discrover/archive/"
-                           version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/maaskola/discrover.git")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "0rah9ja4m0rl5mldd6vag9rwrivw1zrqxssfq8qx64m7961fp68k"))))
+         "173fwi2vb6a5kp406hm3jj6j7v4whww796f2qcygp4rpvamh307y"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f                      ; there are no tests
@@ -2264,106 +2274,102 @@ (define-public discrover
     (license license:gpl3+)))
 
 (define-public eigensoft
-  (let ((revision "1")
-        (commit "b14d1e202e21e532536ff8004f0419cd5e259dc7"))
-    (package
-      (name "eigensoft")
-      (version (string-append "6.1.2-"
-                              revision "."
-                              (string-take commit 9)))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://github.com/DReichLab/EIG.git")
-               (commit commit)))
-         (file-name (string-append "eigensoft-" commit "-checkout"))
-         (sha256
-          (base32
-           "0f5m6k2j5c16xc3xbywcs989xyc26ncy1zfzp9j9n55n9r4xcaiq"))
-         (modules '((guix build utils)))
-         ;; Remove pre-built binaries.
-         (snippet '(begin
-                     (delete-file-recursively "bin")
-                     (mkdir "bin")
-                     #t))))
-      (build-system gnu-build-system)
-      (arguments
-       `(#:tests? #f                    ; There are no tests.
-         #:make-flags '("CC=gcc")
-         #:phases
-         (modify-phases %standard-phases
-           ;; There is no configure phase, but the Makefile is in a
-           ;; sub-directory.
-           (replace 'configure
-             (lambda _
-               (chdir "src")
-               ;; The link flags are incomplete.
-               (substitute* "Makefile"
-                 (("-lgsl") "-lgsl -lm -llapack -llapacke -lpthread"))
-               #t))
-           ;; The provided install target only copies executables to
-           ;; the "bin" directory in the build root.
-           (add-after 'install 'actually-install
-             (lambda* (#:key outputs #:allow-other-keys)
-               (let* ((out (assoc-ref outputs "out"))
-                      (bin  (string-append out "/bin")))
-                 (for-each (lambda (file)
-                             (install-file file bin))
-                           (find-files "../bin" ".*"))
-                 #t))))))
-      (inputs
-       `(("gsl" ,gsl)
-         ("lapack" ,lapack)
-         ("openblas" ,openblas)
-         ("perl" ,perl)
-         ("gfortran" ,gfortran "lib")))
-      (home-page "https://github.com/DReichLab/EIG")
-      (synopsis "Tools for population genetics")
-      (description "The EIGENSOFT package provides tools for population
+  (package
+    (name "eigensoft")
+    (version "7.2.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/DReichLab/EIG.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "1c141fqvhnzibmnf22sv23vbmzm20kjjyrib44cfh75wyndp2d9k"))
+       (modules '((guix build utils)))
+       ;; Remove pre-built binaries.
+       (snippet '(begin
+                   (delete-file-recursively "bin")
+                   (mkdir "bin")
+                   #t))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f                    ; There are no tests.
+       #:make-flags '("CC=gcc")
+       #:phases
+       (modify-phases %standard-phases
+         ;; There is no configure phase, but the Makefile is in a
+         ;; sub-directory.
+         (replace 'configure
+           (lambda _ (chdir "src") #t))
+         ;; The provided install target only copies executables to
+         ;; the "bin" directory in the build root.
+         (add-after 'install 'actually-install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin  (string-append out "/bin")))
+               (for-each (lambda (file)
+                           (install-file file bin))
+                         (find-files "../bin" ".*"))
+               #t))))))
+    (inputs
+     `(("gsl" ,gsl)
+       ("lapack" ,lapack)
+       ("openblas" ,openblas)
+       ("perl" ,perl)
+       ("gfortran" ,gfortran "lib")))
+    (home-page "https://github.com/DReichLab/EIG")
+    (synopsis "Tools for population genetics")
+    (description "The EIGENSOFT package provides tools for population
 genetics and stratification correction.  EIGENSOFT implements methods commonly
 used in population genetics analyses such as PCA, computation of Tracy-Widom
 statistics, and finding related individuals in structured populations.  It
 comes with a built-in plotting script and supports multiple file formats and
 quantitative phenotypes.")
-      ;; The license of the eigensoft tools is Expat, but since it's
-      ;; linking with the GNU Scientific Library (GSL) the effective
-      ;; license is the GPL.
-      (license license:gpl3+))))
+    ;; The license of the eigensoft tools is Expat, but since it's
+    ;; linking with the GNU Scientific Library (GSL) the effective
+    ;; license is the GPL.
+    (license license:gpl3+)))
 
 (define-public edirect
   (package
     (name "edirect")
-    (version "4.10")
+    (version "10.2.20181018")
     (source (origin
               (method url-fetch)
-              (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/"
-                                  "versions/2016-05-03/edirect.tar.gz"))
+              (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect"
+                                  "/versions/" version
+                                  "/edirect-" version ".tar.gz"))
               (sha256
                (base32
-                "15zsprak5yh8c1yrz4r1knmb5s8qcmdid4xdhkh3lqcv64l60hli"))))
+                "091f4aigzpbqih6h82nq566gkp3y07i72yqndmqskfgar1vwgci7"))))
     (build-system perl-build-system)
     (arguments
-     `(#:tests? #f ;no "check" target
-       #:phases
+     `(#:phases
        (modify-phases %standard-phases
          (delete 'configure)
          (delete 'build)
+         (delete 'check)                ; simple check after install
          (replace 'install
-                  (lambda* (#:key outputs #:allow-other-keys)
-                    (let ((target (string-append (assoc-ref outputs "out")
-                                                 "/bin")))
-                      (mkdir-p target)
-                      (install-file "edirect.pl" target)
-                      #t)))
-         (add-after
-          'install 'wrap-program
-          (lambda* (#:key inputs outputs #:allow-other-keys)
-            ;; Make sure 'edirect.pl' finds all perl inputs at runtime.
-            (let* ((out (assoc-ref outputs "out"))
-                   (path (getenv "PERL5LIB")))
-              (wrap-program (string-append out "/bin/edirect.pl")
-                `("PERL5LIB" ":" prefix (,path)))))))))
+           (lambda* (#:key outputs #:allow-other-keys)
+             (install-file "edirect.pl"
+                           (string-append (assoc-ref outputs "out") "/bin"))
+             #t))
+         (add-after 'install 'wrap-program
+           (lambda* (#:key outputs #:allow-other-keys)
+             ;; Make sure 'edirect.pl' finds all perl inputs at runtime.
+             (let* ((out (assoc-ref outputs "out"))
+                    (path (getenv "PERL5LIB")))
+               (wrap-program (string-append out "/bin/edirect.pl")
+                 `("PERL5LIB" ":" prefix (,path))))
+             #t))
+         (add-after 'wrap-program 'check
+           (lambda* (#:key outputs #:allow-other-keys)
+             (invoke (string-append (assoc-ref outputs "out")
+                                    "/bin/edirect.pl")
+                     "-filter" "-help")
+             #t)))))
     (inputs
      `(("perl-html-parser" ,perl-html-parser)
        ("perl-encode-locale" ,perl-encode-locale)
@@ -2379,6 +2385,7 @@ (define-public edirect
        ("perl-net-http" ,perl-net-http)
        ("perl-uri" ,perl-uri)
        ("perl-www-robotrules" ,perl-www-robotrules)
+       ("perl-xml-simple" ,perl-xml-simple)
        ("perl" ,perl)))
     (home-page "http://www.ncbi.nlm.nih.gov/books/NBK179288/")
     (synopsis "Tools for accessing the NCBI's set of databases")
@@ -2474,17 +2481,16 @@ (define-public express
 (define-public express-beta-diversity
   (package
    (name "express-beta-diversity")
-   (version "1.0.7")
+   (version "1.0.8")
    (source (origin
-             (method url-fetch)
-             (uri
-              (string-append
-               "https://github.com/dparks1134/ExpressBetaDiversity/archive/v"
-               version ".tar.gz"))
-             (file-name (string-append name "-" version ".tar.gz"))
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/dparks1134/ExpressBetaDiversity.git")
+                   (commit (string-append "v" version))))
+             (file-name (git-file-name name version))
              (sha256
               (base32
-               "1djvdlmqvjf6h0zq7w36y8cl5cli6rgj86x65znl48agnwmzxfxr"))))
+               "0s0yzg5c21349rh7x4w9266jsvnp7j1hp9cf8sk32hz8nvrj745x"))))
    (build-system gnu-build-system)
    (arguments
     `(#:phases
@@ -2492,17 +2498,13 @@ (define-public express-beta-diversity
         (delete 'configure)
         (add-before 'build 'enter-source (lambda _ (chdir "source") #t))
         (replace 'check
-                 (lambda _ (zero? (system* "../bin/ExpressBetaDiversity"
-                                           "-u"))))
-        (add-after 'check 'exit-source (lambda _ (chdir "..") #t))
+          (lambda _ (invoke "../bin/ExpressBetaDiversity" "-u") #t))
         (replace 'install
-                 (lambda* (#:key outputs #:allow-other-keys)
-                   (let ((bin (string-append (assoc-ref outputs "out")
-                                             "/bin")))
-                     (mkdir-p bin)
-                     (install-file "scripts/convertToEBD.py" bin)
-                     (install-file "bin/ExpressBetaDiversity" bin)
-                     #t))))))
+          (lambda* (#:key outputs #:allow-other-keys)
+            (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+              (install-file "../scripts/convertToEBD.py" bin)
+              (install-file "../bin/ExpressBetaDiversity" bin)
+              #t))))))
    (inputs
     `(("python" ,python-2)))
    (home-page "http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity")
@@ -2535,31 +2537,30 @@ (define-public fasttree
         (delete 'configure)
         (replace 'build
           (lambda* (#:key source #:allow-other-keys)
-            (and (zero? (system* "gcc"
-                                 "-O3"
-                                 "-finline-functions"
-                                 "-funroll-loops"
-                                 "-Wall"
-                                 "-o"
-                                 "FastTree"
-                                 source
-                                 "-lm"))
-                 (zero? (system* "gcc"
-                                 "-DOPENMP"
-                                 "-fopenmp"
-                                 "-O3"
-                                 "-finline-functions"
-                                 "-funroll-loops"
-                                 "-Wall"
-                                 "-o"
-                                 "FastTreeMP"
-                                 source
-                                 "-lm")))))
+            (invoke "gcc"
+                    "-O3"
+                    "-finline-functions"
+                    "-funroll-loops"
+                    "-Wall"
+                    "-o"
+                    "FastTree"
+                    source
+                    "-lm")
+            (invoke "gcc"
+                    "-DOPENMP"
+                    "-fopenmp"
+                    "-O3"
+                    "-finline-functions"
+                    "-funroll-loops"
+                    "-Wall"
+                    "-o"
+                    "FastTreeMP"
+                    source
+                    "-lm")
+            #t))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
-            (let ((bin (string-append (assoc-ref outputs "out")
-                                      "/bin")))
-              (mkdir-p bin)
+            (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
               (install-file "FastTree" bin)
               (install-file "FastTreeMP" bin)
               #t))))))
@@ -2606,38 +2607,39 @@ (define-public fastx-toolkit
 (define-public flexbar
   (package
     (name "flexbar")
-    (version "2.5")
+    (version "3.4.0")
     (source (origin
-              (method url-fetch)
-              (uri
-               (string-append "mirror://sourceforge/flexbar/"
-                              version "/flexbar_v" version "_src.tgz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/seqan/flexbar.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "13jaykc3y1x8y5nn9j8ljnb79s5y51kyxz46hdmvvjj6qhyympmf"))))
+                "1pq9sxvdnldl14libk234m72dqhwgzs3acgl943wchwdqlcsi5r2"))))
     (build-system cmake-build-system)
     (arguments
-     `(#:configure-flags (list
-                          (string-append "-DFLEXBAR_BINARY_DIR="
-                                         (assoc-ref %outputs "out")
-                                         "/bin/"))
-       #:phases
+     `(#:phases
        (modify-phases %standard-phases
          (replace 'check
            (lambda* (#:key outputs #:allow-other-keys)
-             (setenv "PATH" (string-append
-                             (assoc-ref outputs "out") "/bin:"
-                             (getenv "PATH")))
-             (chdir "../flexbar_v2.5_src/test")
-             (zero? (system* "bash" "flexbar_validate.sh"))))
-         (delete 'install))))
+             (setenv "PATH" (string-append (getcwd) ":" (getenv "PATH")))
+             (with-directory-excursion "../source/test"
+               (invoke "bash" "flexbar_test.sh"))
+             #t))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (string-append (assoc-ref outputs "out")))
+                    (bin (string-append out "/bin/")))
+               (install-file "flexbar" bin))
+             #t)))))
     (inputs
      `(("tbb" ,tbb)
        ("zlib" ,zlib)))
     (native-inputs
      `(("pkg-config" ,pkg-config)
        ("seqan" ,seqan)))
-    (home-page "http://flexbar.sourceforge.net")
+    (home-page "https://github.com/seqan/flexbar")
     (synopsis "Barcode and adapter removal tool for sequencing platforms")
     (description
      "Flexbar preprocesses high-throughput nucleotide sequencing data
@@ -2646,7 +2648,7 @@ (define-public flexbar
 read mapping rates and improves genome and transcriptome assemblies.  It
 supports next-generation sequencing data in fasta/q and csfasta/q format from
 Illumina, Roche 454, and the SOLiD platform.")
-    (license license:gpl3)))
+    (license license:bsd-3)))
 
 (define-public fraggenescan
   (package
@@ -3741,75 +3743,48 @@ (define-public jellyfish
 (define-public khmer
   (package
     (name "khmer")
-    (version "2.0")
+    (version "2.1.2")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "khmer" version))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/dib-lab/khmer.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "0wb05shqh77v00256qlm68vbbx3kl76fyzihszbz5nhanl4ni33a"))
-       (patches (search-patches "khmer-use-libraries.patch"))))
+         "02x38d9jw2r58y8dmnj4hffy9wxv1yc1jwbvdbhby9dxndv94r9m"))
+       (patches (search-patches "khmer-use-libraries.patch"))
+       (modules '((guix build utils)))
+       (snippet
+        '(begin
+           ;; Delete bundled libraries.  We do not replace the bundled seqan
+           ;; as it is a modified subset of the old version 1.4.1.
+           ;;
+           ;; We do not replace the bundled MurmurHash as the canonical
+           ;; repository for this code 'SMHasher' is unsuitable for providing
+           ;; a library.  See
+           ;; https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00977.html
+           (delete-file-recursively "third-party/zlib")
+           (delete-file-recursively "third-party/bzip2")
+           #t))))
     (build-system python-build-system)
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'set-paths
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             ;; Delete bundled libraries.
-             (delete-file-recursively "third-party/zlib")
-             (delete-file-recursively "third-party/bzip2")
-             ;; Replace bundled seqan.
-             (let* ((seqan-all "third-party/seqan")
-                    (seqan-include (string-append
-                                    seqan-all "/core/include")))
-               (delete-file-recursively seqan-all)
-               (copy-recursively (string-append (assoc-ref inputs "seqan")
-                                                "/include/seqan")
-                          (string-append seqan-include "/seqan")))
-             ;; We do not replace the bundled MurmurHash as the canonical
-             ;; repository for this code 'SMHasher' is unsuitable for
-             ;; providing a library.  See
-             ;; https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00977.html
-             #t))
          (add-after 'unpack 'set-cc
-           (lambda _
-             (setenv "CC" "gcc")
-             #t))
-         ;; It is simpler to test after installation.
-         (delete 'check)
-         (add-after 'install 'post-install-check
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out")))
-               (setenv "PATH"
-                       (string-append
-                        (getenv "PATH")
-                        ":"
-                        (assoc-ref outputs "out")
-                        "/bin"))
-               (setenv "PYTHONPATH"
-                       (string-append
-                        (getenv "PYTHONPATH")
-                        ":"
-                        out
-                        "/lib/python"
-                        (string-take (string-take-right
-                                      (assoc-ref inputs "python") 5) 3)
-                        "/site-packages"))
-               (with-directory-excursion "build"
-                 (zero? (system* "nosetests" "khmer" "--attr"
-                                 "!known_failing")))))))))
+           (lambda _ (setenv "CC" "gcc") #t))
+         ;; FIXME: This fails with "permission denied".
+         (delete 'reset-gzip-timestamps))))
     (native-inputs
-     `(("seqan" ,seqan)
-       ("python-nose" ,python-nose)))
+     `(("python-cython" ,python-cython)
+       ("python-pytest" ,python-pytest)
+       ("python-pytest-runner" ,python-pytest-runner)))
     (inputs
      `(("zlib" ,zlib)
        ("bzip2" ,bzip2)
        ("python-screed" ,python-screed)
-       ("python-bz2file" ,python-bz2file)
-       ;; Tests fail when gcc-5 is used for compilation.  Use gcc-4.9 at least
-       ;; until the next version of khmer (likely 2.1) is released.
-       ("gcc" ,gcc-4.9)))
+       ("python-bz2file" ,python-bz2file)))
     (home-page "https://khmer.readthedocs.org/")
     (synopsis "K-mer counting, filtering and graph traversal library")
     (description "The khmer software is a set of command-line tools for
@@ -5601,25 +5576,38 @@ (define-public preseq
 (define-public python-screed
   (package
     (name "python-screed")
-    (version "0.9")
+    (version "1.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "screed" version))
        (sha256
         (base32
-         "18czszp9fkx3j6jr7y5kp6dfialscgddk05mw1zkhh2zhn0jd8i0"))))
+         "148vcb7w2wr6a4w6vs2bsxanbqibxfk490zbcbg4m61s8669zdjx"))))
     (build-system python-build-system)
     (arguments
-     `(#:phases
+     '(#:phases
        (modify-phases %standard-phases
-         (replace 'check
-           (lambda _
-             (setenv "PYTHONPATH"
-                     (string-append (getenv "PYTHONPATH") ":."))
-             (zero? (system* "nosetests" "--attr" "!known_failing")))))))
+         ;; Tests must be run after installation, as the "screed" command does
+         ;; not exist right after building.
+         (delete 'check)
+         (add-after 'install 'check
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (setenv "PYTHONPATH"
+                       (string-append out "/lib/python"
+                                      (string-take (string-take-right
+                                                    (assoc-ref inputs "python")
+                                                    5) 3)
+                                      "/site-packages:"
+                                      (getenv "PYTHONPATH")))
+               (setenv "PATH" (string-append out "/bin:" (getenv "PATH"))))
+             (invoke "python" "setup.py" "test")
+             #t)))))
     (native-inputs
-     `(("python-nose" ,python-nose)))
+     `(("python-pytest" ,python-pytest)
+       ("python-pytest-cov" ,python-pytest-cov)
+       ("python-pytest-runner" ,python-pytest-runner)))
     (inputs
      `(("python-bz2file" ,python-bz2file)))
     (home-page "https://github.com/dib-lab/screed/")
@@ -5745,6 +5733,51 @@ (define-public sra-tools
 
 (define-public seqan
   (package
+    (name "seqan")
+    (version "2.4.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/seqan/seqan/releases/"
+                                  "download/seqan-v" version
+                                  "/seqan-library-" version ".tar.xz"))
+              (sha256
+               (base32
+                "19a1rlxx03qy1i1iriicly68w64yjxbv24g9gdywnfmq998v35yx"))))
+    ;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it
+    ;; makes sense to split the outputs.
+    (outputs '("out" "doc"))
+    (build-system trivial-build-system)
+    (arguments
+     `(#:modules ((guix build utils))
+       #:builder
+       (begin
+         (use-modules (guix build utils))
+         (let ((tar (assoc-ref %build-inputs "tar"))
+               (xz  (assoc-ref %build-inputs "xz"))
+               (out (assoc-ref %outputs "out"))
+               (doc (assoc-ref %outputs "doc")))
+           (setenv "PATH" (string-append tar "/bin:" xz "/bin"))
+           (invoke "tar" "xvf" (assoc-ref %build-inputs "source"))
+           (chdir (string-append "seqan-library-" ,version))
+           (copy-recursively "include" (string-append out "/include"))
+           (copy-recursively "share"  (string-append doc "/share"))
+           #t))))
+    (native-inputs
+     `(("source" ,source)
+       ("tar" ,tar)
+       ("xz" ,xz)))
+    (home-page "http://www.seqan.de")
+    (synopsis "Library for nucleotide sequence analysis")
+    (description
+     "SeqAn is a C++ library of efficient algorithms and data structures for
+the analysis of sequences with the focus on biological data.  It contains
+algorithms and data structures for string representation and their
+manipulation, online and indexed string search, efficient I/O of
+bioinformatics file formats, sequence alignment, and more.")
+    (license license:bsd-3)))
+
+(define-public seqan-1
+  (package (inherit seqan)
     (name "seqan")
     (version "1.4.2")
     (source (origin
@@ -5776,16 +5809,7 @@ (define-public seqan
     (native-inputs
      `(("source" ,source)
        ("tar" ,tar)
-       ("bzip2" ,bzip2)))
-    (home-page "http://www.seqan.de")
-    (synopsis "Library for nucleotide sequence analysis")
-    (description
-     "SeqAn is a C++ library of efficient algorithms and data structures for
-the analysis of sequences with the focus on biological data.  It contains
-algorithms and data structures for string representation and their
-manipulation, online and indexed string search, efficient I/O of
-bioinformatics file formats, sequence alignment, and more.")
-    (license license:bsd-3)))
+       ("bzip2" ,bzip2)))))
 
 (define-public seqmagick
   (package
diff --git a/gnu/packages/build-tools.scm b/gnu/packages/build-tools.scm
index 8fcf128135..e1f640ea85 100644
--- a/gnu/packages/build-tools.scm
+++ b/gnu/packages/build-tools.scm
@@ -4,6 +4,7 @@
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
 ;;; Copyright © 2018 Tomáš Čech <sleep_walker@gnu.org>
+;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -98,6 +99,63 @@ (define-public bear
 generate such a compilation database.")
     (license license:gpl3+)))
 
+(define-public gn
+  (let ((commit "f73698ebb33e26a0bf120e2b55d12528fd1dbe7d")
+        (revision "1481"))          ;as returned by `git describe`, used below
+    (package
+      (name "gn")
+      (version (git-version "0.0" revision commit))
+      (home-page "https://gn.googlesource.com/gn")
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference (url home-page) (commit commit)))
+                (sha256
+                 (base32
+                  "078ydwak4424bkqh3hd7q955zxp2c3qlw44lsb29i8jqap140f9d"))
+                (file-name (git-file-name name version))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:tests? #f                    ;FIXME: How to run?
+         #:phases (modify-phases %standard-phases
+                    (add-before 'configure 'set-build-environment
+                      (lambda _
+                        (setenv "CC" "gcc") (setenv "CXX" "g++")
+                        (setenv "AR" "ar")
+                        #t))
+                    (replace 'configure
+                      (lambda _
+                        (invoke "python" "build/gen.py" "--no-sysroot"
+                                "--no-last-commit-position")))
+                    (add-after 'configure 'create-last-commit-position
+                      (lambda _
+                        ;; Create "last_commit_position.h" to avoid a dependency
+                        ;; on 'git' (and the checkout..).
+                        (call-with-output-file "out/last_commit_position.h"
+                          (lambda (port)
+                            (format port
+                                    "#define LAST_COMMIT_POSITION \"~a (~a)\"\n"
+                                    ,revision ,(string-take commit 8))
+                            #t))))
+                    (replace 'build
+                      (lambda _
+                        (invoke "ninja" "-C" "out" "gn"
+                                "-j" (number->string (parallel-job-count)))))
+                    (replace 'install
+                      (lambda* (#:key outputs #:allow-other-keys)
+                        (let ((out (assoc-ref outputs "out")))
+                          (install-file "out/gn" (string-append out "/bin"))
+                          #t))))))
+      (native-inputs
+       `(("ninja" ,ninja)
+         ("python" ,python-2)))
+      (synopsis "Generate Ninja build files")
+      (description
+       "GN is a tool that collects information about a project from @file{.gn}
+files and generates build instructions for the Ninja build system.")
+      ;; GN is distributed as BSD-3, but bundles some files from ICU using the
+      ;; X11 license.
+      (license (list license:bsd-3 license:x11)))))
+
 (define-public meson
   (package
     (name "meson")
diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm
index 77b4dba6d4..29d9a3d6ab 100644
--- a/gnu/packages/crypto.scm
+++ b/gnu/packages/crypto.scm
@@ -94,7 +94,7 @@ (define-public libsodium
 (define-public libmd
   (package
     (name "libmd")
-    (version "1.0.0")
+    (version "1.0.1")
     (source (origin
             (method url-fetch)
             (uri
@@ -105,7 +105,7 @@ (define-public libmd
                              version ".tar.xz")))
             (sha256
              (base32
-              "1iv45npzv0gncjgcpx5m081861zdqxw667ysghqb8721yrlyl6pj"))))
+              "0waclg2d5qin3r26gy5jvy4584ik60njc8pqbzwk0lzq3j9ynkp1"))))
     (build-system gnu-build-system)
     (synopsis "Message Digest functions from BSD systems")
     (description
diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm
index ad1a8638bc..1dcf73771b 100644
--- a/gnu/packages/dns.scm
+++ b/gnu/packages/dns.scm
@@ -569,14 +569,14 @@ (define-public yadifa
 (define-public knot
   (package
     (name "knot")
-    (version "2.7.2")
+    (version "2.7.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://secure.nic.cz/files/knot-dns/"
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "0cc4wgb02ch09x99a1fnr7vsdik8k920q7jafzcamjvy3kpb4w6b"))
+                "1pwjcv7hzhqawisibybma160k77a6f1v94xw6ay9c7j49vrw05w7"))
               (modules '((guix build utils)))
               (snippet
                '(begin
diff --git a/gnu/packages/education.scm b/gnu/packages/education.scm
index 8b02adc182..b333bb9d35 100644
--- a/gnu/packages/education.scm
+++ b/gnu/packages/education.scm
@@ -243,17 +243,17 @@ (define-public tipp10
 (define-public snap
   (package
     (name "snap")
-    (version "4.2.1.4")
+    (version "4.2.2.2")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
-             (url "https://github.com/jmoenig/Snap--Build-Your-Own-Blocks.git")
+             (url "https://github.com/jmoenig/Snap.git")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0yc0w0cdhvi0nwqqrann2v3y0n7shxh7irgixqvlavp4k49d7aqj"))))
+         "0bay08yr58qj8wzpjg33gdj78rfhyskfzidknpdl3cr1jrj6i4p9"))))
     (build-system trivial-build-system)
     (arguments
      `(#:modules ((guix build utils))
@@ -265,7 +265,7 @@ (define-public snap
                 (share (string-append out "/share/snap")))
            (copy-recursively source share)
            ;; Replace the sole minified file in the package.
-           (with-directory-excursion share
+           (with-directory-excursion (string-append share "/src")
              (delete-file "FileSaver.min.js")
              (symlink (string-append (assoc-ref %build-inputs "js-filesaver")
                                      "/share/javascript/FileSaver.min.js")
diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 1069b9e3c3..ce98dbaeb8 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -6,7 +6,7 @@
 ;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
 ;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017, 2018 Chris Marusich <cmmarusich@gmail.com>
-;;; Copyright © 2015, 2016 Christopher Allan Webber <cwebber@dustycloud.org>
+;;; Copyright © 2015, 2016, 2018 Christopher Lemmer Webber <cwebber@dustycloud.org>
 ;;; Copyright © 2016 Adriano Peluso <catonano@gmail.com>
 ;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 David Thompson <davet@gnu.org>
@@ -654,6 +654,33 @@ (define-public emacs-ghub
 only a handful of functions that are not resource-specific.")
     (license license:gpl3+)))
 
+(define-public emacs-scribble-mode
+  (let ((commit "34e9e5edb921813b6483e0fefa848efb6ee4b314")
+        (version "0.0")
+        (revision 0))
+    (package
+      (name "emacs-scribble-mode")
+      (version (if (zero? revision)
+                   version
+                   (string-append version "-"
+                                  (number->string revision)
+                                  "." (string-take commit 7))))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/emacs-pe/scribble-mode.git")
+                      (commit commit)))
+                (sha256
+                 (base32
+                  "0598byqpz2q6yi2q4dwd77jj9z3n99z34d3an51s9m2za0nh1qvp"))))
+      (build-system emacs-build-system)
+      (home-page "https://github.com/emacs-pe/scribble-mode")
+      (synopsis "Emacs mode for editing the Scribble documentation syntax.")
+      (description
+       "This package provides basic syntax highlighting and editing support
+for editing Racket's Scribble documentation syntax in Emacs.")
+      (license license:gpl3+))))
+
 (define-public emacs-haskell-mode
   (package
     (name "emacs-haskell-mode")
@@ -12386,3 +12413,23 @@ (define-public emacs-column-marker
 distances.  Multi-column characters, such as @kbd{TAB} are treated
 correctly.")
     (license license:gpl2+)))
+
+(define-public emacs-slime-repl-ansi-color
+  (let ((commit "ad03263f5d4de473bc173b64a6fc3dc1106393d7"))
+    (package
+      (name "emacs-slime-repl-ansi-color")
+      (version (git-version "0.0.0" "1" commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/deadtrickster/slime-repl-ansi-color")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0bpg7gxz310x7bnlg324c507sxc5gxwwz6h64h6kdq141r73vbi4"))))
+      (build-system emacs-build-system)
+      (home-page "https://github.com/deadtrickster/slime-repl-ansi-color")
+      (synopsis "Color ANSI codes in the REPL of SLIME")
+      (description "Color ANSI codes in the REPL of SLIME")
+      (license license:gpl2+))))
diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index ba37d6afa4..d4df84803b 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -4098,15 +4098,15 @@ (define-public simple-scan
 (define-public eolie
   (package
     (name "eolie")
-    (version "0.9.38")
+    (version "0.9.45")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://gitlab.gnome.org/World/eolie/"
-                                  "uploads/9814c06a1bc83ea09c3da8719a9ed11b/"
+                                  "uploads/020f3f686e2b938731752a1d9f5bfa7e/"
                                   "eolie-" version ".tar.xz"))
               (sha256
                (base32
-                "10vrh91rapgfmqwc6jkcybpmlvn4q0y8bnklw3rddzigf9kvqsff"))))
+                "0371p7g13r0b7zjc48fdcil43ddwpmyvkd2a4vv6ifsqmny6kl42"))))
     (build-system meson-build-system)
     (arguments
      `(#:glib-or-gtk? #t
diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index f058cc79a2..dd83a08038 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -30,6 +30,7 @@
 ;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr>
 ;;; Copyright © 2018 Brendan Tildesley <brendan.tildesley@openmailbox.org>
 ;;; Copyright © 2018 Manuel Graf <graf@init.at>
+;;; Copyright © 2018 Pierre Langlois <pierre.langlois@gmx.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -399,8 +400,8 @@ (define %linux-compatible-systems '("x86_64-linux" "i686-linux" "armhf-linux" "a
 ;; supports qemu "virt" machine and possibly a large number of ARM boards.
 ;; See : https://wiki.debian.org/DebianKernel/ARMMP.
 
-(define %linux-libre-version "4.18.15")
-(define %linux-libre-hash "0v6xs85qn1iy2dj3m6s3cfnhbwb1mjy21d9lagjni8dg3jic26hf")
+(define %linux-libre-version "4.18.16")
+(define %linux-libre-hash "15apfgswp2lrwjpi3vwnanlkdw3q6rkvwrbgrb71rjsy9gazlz62")
 
 (define %linux-libre-4.18-patches
   (list %boot-logo-patch
@@ -430,8 +431,8 @@ (define-public linux-libre
                     #:patches %linux-libre-4.18-patches
                     #:configuration-file kernel-config))
 
-(define %linux-libre-4.14-version "4.14.77")
-(define %linux-libre-4.14-hash "18y81rga2lhsk7bjckglxz52pvnzf103ar0z2zj611g37wyf83r5")
+(define %linux-libre-4.14-version "4.14.78")
+(define %linux-libre-4.14-hash "07dhhw6zdnqn2dznpmkniz58hfkdx89yx7csm9vbx45blnyhjw5z")
 
 (define-public linux-libre-4.14
   (make-linux-libre %linux-libre-4.14-version
@@ -440,14 +441,14 @@ (define-public linux-libre-4.14
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.9
-  (make-linux-libre "4.9.134"
-                    "0f5qif27k0mhc57d98arbfkq7zlvg0ra2gz6g5fasblyjz3j7w7h"
+  (make-linux-libre "4.9.135"
+                    "07v5s6hl08ls2z9xdkbqq1s210mqayfchqbckhp8hlaw089ap71f"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.4
-  (make-linux-libre "4.4.161"
-                    "1q6bsndpjgw72mybhl5l8vrxs4mimg6821bjgi1pjkxbc7nd921b"
+  (make-linux-libre "4.4.162"
+                    "1anb2k9i03369lvbwlw24vimxvk8zpcql4ryz0ydvf3pxv8lirm2"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 
@@ -4167,30 +4168,21 @@ (define-public sysstat
 (define-public light
   (package
     (name "light")
-    (version "1.1.2")
+    (version "1.2")
     (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/haikarainen/light")
-                    (commit version)))
+              (method url-fetch)
+              (uri (string-append
+                     "https://github.com/haikarainen/light/archive/v"
+                     version ".tar.gz"))
               (sha256
                (base32
-                "0c934gxav9cgdf94li6dp0rfqmpday9d33vdn9xb2mfp4war9n4w"))))
+                "1gfvsw7gh5pis733l7j54vzp272pvjyzbg8a0pvapfmg0s7mip97"))
+              (file-name (string-append name "-" version ".tar.gz"))))
     (build-system gnu-build-system)
-    (arguments
-     '(#:tests? #f                      ; no tests
-       #:make-flags (list "CC=gcc"
-                          (string-append "PREFIX=" %output))
-       #:phases
-       (modify-phases %standard-phases
-         (delete 'configure)            ; no configure script
-         (add-after 'unpack 'patch-makefile
-           (lambda _
-             (substitute* "Makefile" (("chown") "#"))
-             #t)))))
     (native-inputs
-     `(("help2man" ,help2man)))
-    (home-page "https://haikarainen.github.io/light")
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)))
+    (home-page "https://haikarainen.github.io/light/")
     (synopsis "GNU/Linux application to control backlights")
     (description
      "Light is a program to send commands to screen backlight controllers
diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm
index c84d26d4cb..c4d0662e99 100644
--- a/gnu/packages/lxqt.scm
+++ b/gnu/packages/lxqt.scm
@@ -5,6 +5,7 @@
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 Nils Gillmann <ng0@n0.is>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Meiyo Peng <meiyo.peng@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -31,30 +32,40 @@ (define-module (gnu packages lxqt)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages kde-frameworks)
   #:use-module (gnu packages pkg-config)
-  #:use-module (gnu packages qt))
+  #:use-module (gnu packages polkit)
+  #:use-module (gnu packages qt)
+  #:use-module (gnu packages xorg))
 
 (define-public libqtxdg
   (package
     (name "libqtxdg")
-    (version "1.2.0")
+    (version "3.2.0")
     (source
      (origin
        (method url-fetch)
-       (uri
-         (string-append "https://github.com/lxde/libqtxdg/releases/"
-                        "download/" version "/" name "-" version ".tar.xz"))
+       (uri (string-append
+             "https://github.com/lxqt/" name "/releases/download/"
+             version "/" name "-" version ".tar.xz"))
        (sha256
-        (base32
-         "1ncqs0lcll5nx69hxfg33m3jfkryjqrjhr2kdci0b8pyaqdv1jc8"))))
+        (base32 "0lq548pa69hfvnbj2ypba5ygm8n6v6g7bqqm8p5g538l1l3394cl"))))
     (build-system cmake-build-system)
     (arguments
-     `(#:tests? #f ; test fails with message "Exception"
-       #:configure-flags '("-DBUILD_TESTS=ON")))
-    (native-inputs
-     `(("pkg-config" ,pkg-config)))
+     `(#:configure-flags
+       `("-DBUILD_TESTS=ON"
+         ,(string-append "-DQTXDGX_ICONENGINEPLUGIN_INSTALL_PATH="
+                         %output "/lib/qt5/plugins/iconengines"))
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'pre-check
+           (lambda _
+             ;; Run the tests offscreen.
+             (setenv "QT_QPA_PLATFORM" "offscreen")
+             #t)))))
     (propagated-inputs
-     `(("qtbase" ,qtbase))) ; according to Qt5Xdg.pc
-    (home-page "https://github.com/lxde/libqtxdg")
+     ;; required by Qt5XdgIconLoader.pc
+     `(("qtbase" ,qtbase)
+       ("qtsvg" ,qtsvg)))
+    (home-page "https://github.com/lxqt/libqtxdg")
     (synopsis "Qt implementation of freedesktop.org xdg specifications")
     (description "Libqtxdg implements the freedesktop.org xdg specifications
 in Qt.")
@@ -63,29 +74,40 @@ (define-public libqtxdg
 (define-public liblxqt
   (package
     (name "liblxqt")
-    (version "0.9.0")
+    (version "0.13.0")
     (source
      (origin
        (method url-fetch)
-       (uri
-         (string-append "https://github.com/lxde/" name
-                        "/archive/" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (uri (string-append
+             "https://github.com/lxqt/" name "/releases/download/"
+             version "/" name "-" version ".tar.xz"))
        (sha256
-        (base32
-         "0mbl3qc0yfgfsndqrw8vg8k5irsy0pg2wrad8nwv0aphphd4n7rg"))
-       (patches (search-patches "liblxqt-include.patch"))))
+        (base32 "0fba0nq5b9fvvmklcikcd4nwhzlp5d6k1q1f80r34kncdzfvj7dl"))))
     (build-system cmake-build-system)
     (arguments
-     `(#:tests? #f))
-    (native-inputs `(("pkg-config" ,pkg-config)))
+     `(#:tests? #f                      ; no tests
+       #:configure-flags
+       ;; TODO: prefetch translations files from 'lxqt-l10n'.
+       '("-DPULL_TRANSLATIONS=NO")
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-source
+           (lambda _
+             (substitute* "CMakeLists.txt"
+               (("DESTINATION \"\\$\\{POLKITQT-1_POLICY_FILES_INSTALL_DIR\\}")
+                "DESTINATION \"${CMAKE_INSTALL_PREFIX}/share/polkit-1/actions"))
+             #t)))))
     (inputs
      `(("kwindowsystem" ,kwindowsystem)
        ("libqtxdg" ,libqtxdg)
-       ("qtbase" ,qtbase)
+       ("libxscrnsaver" ,libxscrnsaver)
+       ("polkit-qt" ,polkit-qt)
+       ("qtsvg" ,qtsvg)
        ("qttools" ,qttools)
        ("qtx11extras" ,qtx11extras)))
-    (home-page "http://lxqt.org/")
+    (native-inputs
+     `(("lxqt-build-tools" ,lxqt-build-tools)))
+    (home-page "https://lxqt.org/")
     (synopsis "Core utility library for all LXQt components")
     (description "liblxqt provides the basic libraries shared by the
 components of the LXQt desktop environment.")
diff --git a/gnu/packages/mpd.scm b/gnu/packages/mpd.scm
index 3e69ddba69..b69be2965f 100644
--- a/gnu/packages/mpd.scm
+++ b/gnu/packages/mpd.scm
@@ -58,7 +58,7 @@ (define-module (gnu packages mpd)
 (define-public libmpdclient
   (package
     (name "libmpdclient")
-    (version "2.15")
+    (version "2.16")
     (source (origin
               (method url-fetch)
               (uri
@@ -67,7 +67,7 @@ (define-public libmpdclient
                               "/libmpdclient-" version ".tar.xz"))
               (sha256
                (base32
-                "1la60ar6i4ghpscrlgm45kci9b74bvkpsfybhg0ygs4rzpwzdnxl"))))
+                "0r24cl3i9nvs6a47mvwaxk1kb5wmnhkhrw1q5cq9010fgjvdlszs"))))
     (build-system meson-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)
diff --git a/gnu/packages/patches/crossmap-allow-system-pysam.patch b/gnu/packages/patches/crossmap-allow-system-pysam.patch
deleted file mode 100644
index 611c4ff74d..0000000000
--- a/gnu/packages/patches/crossmap-allow-system-pysam.patch
+++ /dev/null
@@ -1,121 +0,0 @@
-This patch modifies the build process such that the bundled copy of pysam does
-not need to be built if CROSSMAP_USE_SYSTEM_PYSAM is set and the pysam module
-can be imported.
-
-Upstream has agreed to apply the patch in the next maintenance release of
-crossmap.  The patch has already been uploaded to
-http://sourceforge.net/projects/crossmap/files/patch/.
-
-diff --git a/setup.py b/setup.py
---- a/setup.py	2015-02-26 15:28:49.771189185 +0100
-+++ b/setup.py	2015-02-26 15:55:03.440327752 +0100
-@@ -19,6 +19,15 @@
- except:
- 	have_numpy = False
- 
-+try:
-+	import pysam
-+	if os.environ['CROSSMAP_USE_SYSTEM_PYSAM']:
-+		have_pysam = True
-+	else:
-+		have_pysam = False
-+except ImportError:
-+	have_pysam = False
-+
- if platform.system()=='Windows':
- 	print >> sys.stderr, "Sorry, Windows platform is not supported!"
- 	sys.exit()
-@@ -165,49 +174,50 @@
- 	
- 	
- 	#================= pysam samtools ====================
--	extensions.append(Extension(
--    	"pysam.csamtools",              
--		csamtools_sources + [ "lib/pysam/%s" % x for x in ("pysam_util.c", )] +\
--		glob.glob( os.path.join( "lib/samtools", "*.pysam.c" )) +\
--		os_c_files + \
--		glob.glob( os.path.join( "lib/samtools", "*", "*.pysam.c" ) ),
--		library_dirs=[],
--		include_dirs=[ "lib/samtools", "lib/pysam" ] + include_os,
--		libraries=[ "z", ],
--		language="c",
--		define_macros = [('_FILE_OFFSET_BITS','64'),('_USE_KNETFILE','')], 
--    ))
--
--	extensions.append(Extension(
--		"pysam.ctabix",                   
--		tabix_sources + [ "lib/pysam/%s" % x for x in ( "tabix_util.c", )] +\
--		os_c_files + \
--		glob.glob( os.path.join( "lib/tabix", "*.pysam.c" ) ),
--		library_dirs=[],
--		include_dirs=[ "lib/tabix", "lib/pysam" ] + include_os,
--		libraries=[ "z", ],
--		language="c",
--		define_macros = [('_FILE_OFFSET_BITS','64'),
--                     ('_USE_KNETFILE','')], 
--    ))
--
--	extensions.append(Extension(
--		"pysam.TabProxies",               
--		tabproxies_sources + os_c_files,
--		library_dirs=[],
--		include_dirs= include_os,
--		libraries=[ "z", ],
--		language="c",
--    ))
--
--	extensions.append(Extension(
--		"pysam.cvcf",                   
--		cvcf_sources + os_c_files,
--		library_dirs=[],
--		include_dirs= ["lib/tabix",] + include_os,
--		libraries=[ "z", ],
--		language="c",
--    ))
-+        if not have_pysam:
-+                extensions.append(Extension(
-+                        "pysam.csamtools",              
-+                        csamtools_sources + [ "lib/pysam/%s" % x for x in ("pysam_util.c", )] +\
-+                        glob.glob( os.path.join( "lib/samtools", "*.pysam.c" )) +\
-+                        os_c_files + \
-+                        glob.glob( os.path.join( "lib/samtools", "*", "*.pysam.c" ) ),
-+                        library_dirs=[],
-+                        include_dirs=[ "lib/samtools", "lib/pysam" ] + include_os,
-+                        libraries=[ "z", ],
-+                        language="c",
-+                        define_macros = [('_FILE_OFFSET_BITS','64'),('_USE_KNETFILE','')], 
-+                ))
-+
-+                extensions.append(Extension(
-+                        "pysam.ctabix",                   
-+                        tabix_sources + [ "lib/pysam/%s" % x for x in ( "tabix_util.c", )] +\
-+                        os_c_files + \
-+                        glob.glob( os.path.join( "lib/tabix", "*.pysam.c" ) ),
-+                        library_dirs=[],
-+                        include_dirs=[ "lib/tabix", "lib/pysam" ] + include_os,
-+                        libraries=[ "z", ],
-+                        language="c",
-+                        define_macros = [('_FILE_OFFSET_BITS','64'),
-+                                         ('_USE_KNETFILE','')], 
-+                ))
-+
-+                extensions.append(Extension(
-+                        "pysam.TabProxies",               
-+                        tabproxies_sources + os_c_files,
-+                        library_dirs=[],
-+                        include_dirs= include_os,
-+                        libraries=[ "z", ],
-+                        language="c",
-+                ))
-+
-+                extensions.append(Extension(
-+                        "pysam.cvcf",                   
-+                        cvcf_sources + os_c_files,
-+                        library_dirs=[],
-+                        include_dirs= ["lib/tabix",] + include_os,
-+                        libraries=[ "z", ],
-+                        language="c",
-+                ))
- 
- 
- 	return extensions     
diff --git a/gnu/packages/patches/delly-use-system-libraries.patch b/gnu/packages/patches/delly-use-system-libraries.patch
deleted file mode 100644
index 3315c2a176..0000000000
--- a/gnu/packages/patches/delly-use-system-libraries.patch
+++ /dev/null
@@ -1,56 +0,0 @@
---- a/Makefile	2017-04-09 12:48:15.000000000 +0200
-+++ b/Makefile	2017-06-21 14:26:02.749282787 +0200
-@@ -9,8 +9,8 @@
- 
- # Flags
- CXX=g++
--CXXFLAGS += -isystem ${SEQTK_ROOT} -isystem ${BOOST_ROOT} -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing
--LDFLAGS += -L${SEQTK_ROOT} -L${BOOST_ROOT}/stage/lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time 
-+CXXFLAGS += -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing
-+LDFLAGS += -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time 
- 
- # Additional flags for release/debug
- ifeq (${PARALLEL}, 1)
-@@ -23,7 +23,7 @@
- ifeq (${STATIC}, 1)
- 	LDFLAGS += -static -static-libgcc -pthread -lhts -lz
- else
--	LDFLAGS += -lhts -lz -Wl,-rpath,${SEQTK_ROOT},-rpath,${BOOST_ROOT}/stage/lib
-+	LDFLAGS += -lhts -lz
- endif
- ifeq (${DEBUG}, 1)
- 	CXXFLAGS += -g -O0 -fno-inline -DDEBUG
-@@ -41,29 +41,17 @@
- DELLYSOURCES = $(wildcard src/*.h) $(wildcard src/*.cpp)
- 
- # Targets
--TARGETS = .htslib .bcftools .boost src/delly src/cov src/dpe
-+TARGETS = src/delly src/cov src/dpe
- 
- all:   	$(TARGETS)
- 
--.htslib: $(HTSLIBSOURCES)
--	cd src/htslib && make && make lib-static && cd ../../ && touch .htslib
--
--.bcftools: $(HTSLIBSOURCES)
--	cd src/bcftools && make && cd ../../ && touch .bcftools
--
--.boost: $(BOOSTSOURCES)
--	cd src/modular-boost && ./bootstrap.sh --prefix=${PWD}/src/modular-boost --without-icu --with-libraries=iostreams,filesystem,system,program_options,date_time && ./b2 && ./b2 headers && cd ../../ && touch .boost
--
--src/delly: .htslib .bcftools .boost $(DELLYSOURCES)
--	$(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
--
--src/cov: .htslib .bcftools .boost $(DELLYSOURCES)
-+src/cov: $(DELLYSOURCES)
- 	$(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
- 
--src/dpe: .htslib .bcftools .boost $(DELLYSOURCES)
-+src/dpe: $(DELLYSOURCES)
- 	$(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
- 
- clean:
- 	cd src/htslib && make clean
- 	cd src/modular-boost && ./b2 --clean-all
--	rm -f $(TARGETS) $(TARGETS:=.o) .htslib .boost .bcftools
-+	rm -f $(TARGETS) $(TARGETS:=.o)
diff --git a/gnu/packages/patches/liblxqt-include.patch b/gnu/packages/patches/liblxqt-include.patch
deleted file mode 100644
index 4e8cf04789..0000000000
--- a/gnu/packages/patches/liblxqt-include.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-Patch to fix build with Qt 5.5, taken from upstream:
-   https://github.com/lxde/liblxqt/commit/7303ea207de0771d6f450a31ec4a1ce69202869b
-
-diff -u -r liblxqt-0.9.0.orig/lxqtnotification.h liblxqt-0.9.0/lxqtnotification.h
---- liblxqt-0.9.0.orig/lxqtnotification.h	2015-07-27 22:49:05.365166482 +0200
-+++ liblxqt-0.9.0/lxqtnotification.h	2015-07-27 22:49:36.897606619 +0200
-@@ -25,6 +25,7 @@
- #ifndef LXQTNOTIFICATION_H
- #define LXQTNOTIFICATION_H
- 
-+#include <QObject>
- #include <QStringList>
- #include "lxqtglobals.h"
- 
diff --git a/gnu/packages/patches/tophat-build-with-later-seqan.patch b/gnu/packages/patches/tophat-build-with-later-seqan.patch
deleted file mode 100644
index fc742e2a7d..0000000000
--- a/gnu/packages/patches/tophat-build-with-later-seqan.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-This patch resolves a build failure when building TopHat 2.1.0 with SeqAn 1.4.
-This is the relevant part of a patch originally posted here:
-https://lists.fu-berlin.de/pipermail/seqan-dev/2014-July/msg00001.html
-
---- a/src/segment_juncs.cpp
-+++ b/src/segment_juncs.cpp
-@@ -2050,10 +2050,13 @@ void juncs_from_ref_segs(RefSequenceTabl
-     typedef map<uint32_t, IntronMotifs> MotifMap;
-     
-     MotifMap ims;
--	
--    seqan::DnaStringReverseComplement rev_donor_dinuc(donor_dinuc);
--    seqan::DnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc);
--    
-+
-+    typedef seqan::ModifiedString<
-+                    seqan::ModifiedString<seqan::DnaString const, seqan::ModView<seqan::FunctorComplement<seqan::Dna> > >,  
-+                    seqan::ModReverse>   ConstDnaStringReverseComplement;
-+    ConstDnaStringReverseComplement rev_donor_dinuc(donor_dinuc);
-+    ConstDnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc);
-+     
-     if (talkative)
-         fprintf(stderr, "Collecting potential splice sites in islands\n");
- 
diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm
index d773b2f948..f407276ac5 100644
--- a/gnu/packages/python-crypto.scm
+++ b/gnu/packages/python-crypto.scm
@@ -850,16 +850,15 @@ (define-public python2-pycryptodome
 (define-public python-m2crypto
   (package
     (name "python-m2crypto")
-    (version "0.29.0")
+    (version "0.30.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "M2Crypto" version))
        (sha256
-        (base32 "1h16gpilrnlzc0iyj1mnd1iqh8wchzjsxjqw9n344glimg2s5zm0"))))
+        (base32 "1iizrpkn4c2n70nvcjqlmnk6fz3vddkrjmwavz1zlsnwv8f7bcm1"))))
     (build-system python-build-system)
     (inputs `(("openssl" ,openssl)))
-    (propagated-inputs `(("python-typing" ,python-typing)))
     (home-page "https://gitlab.com/m2crypto/m2crypto")
     (synopsis "Python crypto and TLS toolkit")
     (description "@code{M2Crypto} is a complete Python wrapper for OpenSSL
@@ -869,10 +868,15 @@ (define-public python-m2crypto
 AuthCookies for web session management; FTP/TLS client and server; S/MIME;
 M2Crypto can also be used to provide TLS for Twisted.  Smartcards supported
 through the Engine interface.")
+    (properties `((python2-variant . ,(delay python2-m2crypto))))
     (license license:expat)))
 
 (define-public python2-m2crypto
-  (package-with-python2 python-m2crypto))
+  (let ((m2crypto (package-with-python2
+                   (strip-python2-variant python-m2crypto))))
+    (package (inherit m2crypto)
+             (propagated-inputs
+              `(("python2-typing" ,python2-typing))))))
 
 (define-public python-pylibscrypt
   (package
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 2b6a0647fd..99b214f3bc 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -55,6 +55,7 @@
 ;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
 ;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2018 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2018 Luther Thompson <lutheroto@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -5904,14 +5905,14 @@ (define-public python2-flake8-polyfill
 (define-public python-mistune
   (package
     (name "python-mistune")
-    (version "0.8.3")
+    (version "0.8.4")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "mistune" version))
        (sha256
         (base32
-         "06b662p6kf46wh2jsabaqhaq4bz1srh2zxkrnx4yg96azlxw645w"))))
+         "0vkmsh0x480rni51lhyvigfdf06b9247z868pk3bal1wnnfl58sr"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-nose" ,python-nose)
@@ -5928,25 +5929,19 @@ (define-public python2-mistune
 (define-public python-markdown
   (package
     (name "python-markdown")
-    (version "2.6.11")
+    (version "3.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "Markdown" version))
        (sha256
         (base32
-         "108g80ryzykh8bj0i7jfp71510wrcixdi771lf2asyghgyf8cmm8"))))
+         "0z6v8649sr434d5r5zmrhydka7v7f9yas4bwcgkcs0650jdhybnh"))))
     (build-system python-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-                  (lambda _
-                    (zero? (system* "python" "run-tests.py")))))))
     (native-inputs
      `(("python-nose" ,python-nose)
        ("python-pyyaml" ,python-pyyaml)))
-    (home-page "https://pythonhosted.org/Markdown/")
+    (home-page "https://python-markdown.github.io/")
     (synopsis "Python implementation of Markdown")
     (description
      "This package provides a Python implementation of John Gruber's
@@ -9462,13 +9457,13 @@ (define-public python2-cleo
 (define-public python-lazy-object-proxy
   (package
     (name "python-lazy-object-proxy")
-    (version "1.2.2")
+    (version "1.3.1")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "lazy-object-proxy" version))
               (sha256
                (base32
-                "0s22aqqkdscyh8sjspyyax7qa1aiz8p4midrnyf39717fhfczm6x"))))
+                "0yha7q9bhw857fwaby785d63mffhngl9npwzlk9i0pwlkwvbx4gb"))))
     (build-system python-build-system)
     (home-page "https://github.com/ionelmc/python-lazy-object-proxy")
     (synopsis "Lazy object proxy for python")
@@ -9950,13 +9945,13 @@ (define-public python2-nltk
 (define-public python-pymongo
   (package
     (name "python-pymongo")
-    (version "3.3.0")
+    (version "3.7.2")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "pymongo" version))
               (sha256
                (base32
-                "07mra6w86wjqy4lx5fvimidjhhfzd562gfjn8grsnbv2q8pk0i9x"))))
+                "0zis4707r9hdg5qgkhp3wss9camr9h56ixyfc8n9dxwlnnly4x4c"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-certifi" ,python-certifi)))
@@ -11849,14 +11844,14 @@ (define-public python2-radon
 (define-public python-sure
   (package
     (name "python-sure")
-    (version "1.4.6")
+    (version "1.4.11")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "sure" version))
        (sha256
         (base32
-         "1iyqsy2d6radi88g1qf0lziy5b39h5cpb3g5jiqyb4xi46ig3x1z"))))
+         "1and0drq8w9iplsic22n2h7hkpyq03a1mbqk4sgcdqhqzdqm539w"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-mock" ,python-mock)
@@ -14429,3 +14424,28 @@ (define-public python-dask
 larger-than-memory or distributed environments.  These parallel collections
 run on top of the dynamic task schedulers. ")
     (license license:bsd-3)))
+
+(define-public python-ilinkedlist
+  (package
+    (name "python-ilinkedlist")
+    (version "0.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "ilinkedlist" version))
+       (sha256
+        (base32
+         "063c2gm4jkgkv0nsg7mrc8y0w82ms98l4xchmbrvr68cscglhk69"))))
+    (build-system python-build-system)
+    (native-inputs `(("python-pytest" ,python-pytest)))
+    (inputs `(("python" ,python)))
+    (home-page "https://github.com/luther9/ilinkedlist-py")
+    (synopsis "Immutable linked list library")
+    (description
+     "This is a implementation of immutable linked lists for Python.  It
+contains @code{nil} (the empty linked list) and a @code{Pair} class for nodes.
+Since a linked list is treated as immutable, it is hashable, and its length
+can be retrieved in constant time.  Some of the terminology is inspired by
+LISP.  It is possible to create an improper list by creating a @code{Pair}
+with a non-list @code{cdr}.")
+    (license license:gpl3+)))
diff --git a/gnu/packages/samba.scm b/gnu/packages/samba.scm
index 65d41a2b67..470643ec4f 100644
--- a/gnu/packages/samba.scm
+++ b/gnu/packages/samba.scm
@@ -150,14 +150,14 @@ (define (install dir)
 (define-public samba
   (package
     (name "samba")
-    (version "4.8.5")
+    (version "4.8.6")
     (source (origin
              (method url-fetch)
              (uri (string-append "https://download.samba.org/pub/samba/stable/"
                                  "samba-" version ".tar.gz"))
              (sha256
               (base32
-               "0mailvhjsma19k6b6zjl02z9n2hbbyfybvicjfw2hh9d4sqyd3p5"))))
+               "15hawqdm37l6lp9k14c634315p77cllsx89bvbw9h38fg1hj3fbk"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
diff --git a/gnu/packages/ssh.scm b/gnu/packages/ssh.scm
index 816324b279..3d95b2e849 100644
--- a/gnu/packages/ssh.scm
+++ b/gnu/packages/ssh.scm
@@ -134,14 +134,14 @@ (define-public libssh2
 (define-public openssh
   (package
    (name "openssh")
-   (version "7.8p1")
+   (version "7.9p1")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://openbsd/OpenSSH/portable/"
                                  name "-" version ".tar.gz"))
              (sha256
               (base32
-               "1jj4f586r9lhakp2w0zv7j616d6x62m15q8l4nxq7haja6qlnj0s"))))
+               "1b8sy6v0b8v4ggmknwcqx3y1rjcpsll0f1f8f4vyv11x4ni3njvb"))))
    (build-system gnu-build-system)
    (native-inputs `(("groff" ,groff)))
    (inputs `(("openssl" ,openssl)
diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index 294d334423..cbe601ea9d 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -2288,6 +2288,44 @@ (define-public texlive-latex-capt-of
 to something that's not a float.")
     (license license:lppl)))
 
+(define-public texlive-latex-doi
+  (package
+    (name "texlive-latex-doi")
+    (version (number->string %texlive-revision))
+    (source (origin
+              (method svn-fetch)
+              (uri (svn-reference
+                    (url (string-append "svn://www.tug.org/texlive/tags/"
+                                        %texlive-tag "/Master/texmf-dist/"
+                                        "/tex/latex/doi"))
+                    (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
+              (sha256
+               (base32
+                "0378rdmrgr2lzbfi4qqy4dfpj5im20diyd8z8b9m4mlg05r7wgnb"))))
+    (build-system trivial-build-system)
+    (arguments
+     `(#:modules ((guix build utils))
+       #:builder
+       (begin
+         (use-modules (guix build utils))
+         (let ((target (string-append (assoc-ref %outputs "out")
+                                      "/share/texmf-dist/tex/latex/doi")))
+           (mkdir-p target)
+           (copy-recursively (assoc-ref %build-inputs "source") target)
+           #t))))
+    (home-page "https://www.ctan.org/pkg/doi")
+    (synopsis "Create correct hyperlinks for DOI numbers")
+    (description
+     "You can hyperlink DOI numbers to doi.org.  However, some publishers have
+elected to use nasty characters in their DOI numbering scheme (@code{<},
+@code{>}, @code{_} and @code{;} have all been spotted).  This will either
+upset LaTeX, or your PDF reader.  This package contains a single user-level
+command @code{\\doi{}}, which takes a DOI number, and creates a correct
+hyperlink to the target of the DOI.")
+    ;; Any version of the LPPL.
+    (license license:lppl1.3+)))
+
 (define-public texlive-latex-etoolbox
   (package
     (name "texlive-latex-etoolbox")
@@ -4751,3 +4789,154 @@ (define-public texlive-latex-koma-script
 refers to the version of scrbook, scrreprt, scrartcl, scrlttr2 and
 typearea (which are the main parts of the bundle).")
     (license license:lppl1.3+)))
+
+(define-public texlive-generic-listofitems
+  (package
+    (name "texlive-generic-listofitems")
+    (version (number->string %texlive-revision))
+    (source (origin
+              (method svn-fetch)
+              (uri (svn-reference
+                    (url (string-append "svn://www.tug.org/texlive/tags/"
+                                        %texlive-tag "/Master/texmf-dist/"
+                                        "/tex/generic/listofitems"))
+                    (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
+              (sha256
+               (base32
+                "1k50z6ixgwwzy84mi0dr5vcjah5p7wvgq66y45bilm91a4m8sgla"))))
+    (build-system trivial-build-system)
+    (arguments
+     `(#:modules ((guix build utils))
+       #:builder
+       (begin
+         (use-modules (guix build utils))
+         (let ((target (string-append (assoc-ref %outputs "out")
+                                      "/share/texmf-dist/tex/generic/listofitems")))
+           (mkdir-p target)
+           (copy-recursively (assoc-ref %build-inputs "source") target)
+           #t))))
+    (home-page "https://www.ctan.org/pkg/listofitems")
+    (synopsis "Grab items in lists using user-specified seperation character")
+    (description
+     "This package allows one to capture all the items of a list, for which
+the parsing character has been selected by the user, and to access any of
+these items with a simple syntax.")
+    (license license:lppl1.3c+)))
+
+(define-public texlive-latex-readarray
+  (package
+    (name "texlive-latex-readarray")
+    (version (number->string %texlive-revision))
+    (source (origin
+              (method svn-fetch)
+              (uri (svn-reference
+                    (url (string-append "svn://www.tug.org/texlive/tags/"
+                                        %texlive-tag "/Master/texmf-dist/"
+                                        "/tex/latex/readarray"))
+                    (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
+              (sha256
+               (base32
+                "0c53k180ivn1n7fz3ngvd2w1i5dw3kxml0n64vhki88xsylz7lxp"))))
+    (build-system trivial-build-system)
+    (arguments
+     `(#:modules ((guix build utils))
+       #:builder
+       (begin
+         (use-modules (guix build utils))
+         (let ((target (string-append (assoc-ref %outputs "out")
+                                      "/share/texmf-dist/tex/latex/readarray")))
+           (mkdir-p target)
+           (copy-recursively (assoc-ref %build-inputs "source") target)
+           #t))))
+    (propagated-inputs
+     `(("texlive-generic-listofitems" ,texlive-generic-listofitems)))
+    (home-page "https://www.ctan.org/pkg/readarray")
+    (synopsis "Read, store and recall array-formatted data")
+    (description
+     "This package allows the user to input formatted data into elements of a
+2-D or 3-D array and to recall that data at will by individual cell number.
+The data can be but need not be numerical in nature.  It can be, for example,
+formatted text.")
+    (license license:lppl1.3)))
+
+(define-public texlive-latex-verbatimbox
+  (package
+    (name "texlive-latex-verbatimbox")
+    (version (number->string %texlive-revision))
+    (source (origin
+              (method svn-fetch)
+              (uri (svn-reference
+                    (url (string-append "svn://www.tug.org/texlive/tags/"
+                                        %texlive-tag "/Master/texmf-dist/"
+                                        "/tex/latex/verbatimbox"))
+                    (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
+              (sha256
+               (base32
+                "0qh1cgvfs463zsi2pjg490gj0mkjfdpfc381j10cbb5la304psna"))))
+    (build-system trivial-build-system)
+    (arguments
+     `(#:modules ((guix build utils))
+       #:builder
+       (begin
+         (use-modules (guix build utils))
+         (let ((target (string-append (assoc-ref %outputs "out")
+                                      "/share/texmf-dist/tex/latex/verbatimbox")))
+           (mkdir-p target)
+           (copy-recursively (assoc-ref %build-inputs "source") target)
+           #t))))
+    (propagated-inputs
+     `(("texlive-latex-readarray" ,texlive-latex-readarray)))
+    (home-page "https://www.ctan.org/pkg/verbatimbox")
+    (synopsis "Deposit verbatim text in a box")
+    (description
+     "The package provides a @code{verbbox} environment to place its contents
+into a globally available box, or into a box specified by the user.  The
+global box may then be used in a variety of situations (for example, providing
+a replica of the @code{boxedverbatim} environment itself).  A valuable use is
+in places where the standard @code{verbatim} environment (which is based on a
+@code{trivlist}) may not appear.")
+    (license license:lppl1.3+)))
+
+(define-public texlive-latex-examplep
+  (package
+    (name "texlive-latex-examplep")
+    (version (number->string %texlive-revision))
+    (source (origin
+              (method svn-fetch)
+              (uri (svn-reference
+                    (url (string-append "svn://www.tug.org/texlive/tags/"
+                                        %texlive-tag "/Master/texmf-dist/"
+                                        "/tex/latex/examplep"))
+                    (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
+              (sha256
+               (base32
+                "0fsvvmz68ij0zwfzrny6x13d92grxr4ap59lxgah4smbkccd6s27"))))
+    (build-system trivial-build-system)
+    (arguments
+     `(#:modules ((guix build utils))
+       #:builder
+       (begin
+         (use-modules (guix build utils))
+         (let ((target (string-append (assoc-ref %outputs "out")
+                                      "/share/texmf-dist/tex/latex/examplep")))
+           (mkdir-p target)
+           (copy-recursively (assoc-ref %build-inputs "source") target)
+           #t))))
+    (home-page "https://www.ctan.org/pkg/examplep")
+    (synopsis "Verbatim phrases and listings in LaTeX")
+    (description
+     "Examplep provides sophisticated features for typesetting verbatim source
+code listings, including the display of the source code and its compiled LaTeX
+or METAPOST output side-by-side, with automatic width detection and enabled
+page breaks (in the source), without the need for specifying the source twice.
+Special care is taken that section, page and footnote numbers do not interfere
+with the main document.  For typesetting short verbatim phrases, a replacement
+for the @code{\\verb} command is also provided in the package, which can be
+used inside tables and moving arguments such as footnotes and section
+titles.")
+    ;; No version of the GPL is specified.
+    (license license:gpl3+)))
diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index a6930abfda..4fcd15e4aa 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -2645,7 +2645,7 @@ (define-public mediainfo
 (define-public livemedia-utils
   (package
     (name "livemedia-utils")
-    (version "2017.10.28")
+    (version "2018.10.17")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2653,7 +2653,7 @@ (define-public livemedia-utils
                     version ".tar.gz"))
               (sha256
                (base32
-                "0f5kxpayqn3yhabqrd2cqlc74i6x2xr01jfkank1lcilxnfyrsnq"))
+                "1s69ipvdc6ldscp0cr1zpsll8xc3qcagr95nl84x7b1rbg4xjs3w"))
               (modules '((guix build utils)))
               (snippet '(begin
                           ;; As of glibc 2.26, <xlocale.h> no longer is.
diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index 1af8fed5e7..5366c27fec 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -2448,7 +2448,7 @@ (define-public xf86-input-evdev
 (define-public xf86-input-libinput
   (package
     (name "xf86-input-libinput")
-    (version "0.28.0")
+    (version "0.28.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2456,7 +2456,7 @@ (define-public xf86-input-libinput
                     name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "189h8vl0005yizwrs4d0sng6j8lwkd3xi1zwqg8qavn2bw34v691"))))
+                "12yr0yki94j2416bfhmkz5jpacffm27jkra89fl7h03c0y749nls"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags
@@ -5065,7 +5065,7 @@ (define-public libxcb
 (define-public xorg-server
   (package
     (name "xorg-server")
-    (version "1.20.1")
+    (version "1.20.2")
     (source
       (origin
         (method url-fetch)
@@ -5074,7 +5074,7 @@ (define-public xorg-server
               name "-" version ".tar.bz2"))
         (sha256
          (base32
-          "0679942x1ma2p30vlvqylpjc5v1ak1pgqysnqrj82nz7dzl9zjar"))
+          "1qnf7jdygdgbgjfm5mfr691dl8d56mpssa82mvhm8bzj92yggm8f"))
         (patches
          (list
           ;; See: