Merge branch 'staging' into core-updates

0 files changed, 0 insertions, 0 deletions
diff --git a/gnu/local.mk b/gnu/local.mk
index 2a6908d4bb..3be9c9d60e 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -15,7 +15,7 @@
 # Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 # Copyright © 2017, 2018 Clément Lassieur <clement@lassieur.org>
 # Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
-# Copyright © 2017, 2018 Gábor Boskovits <boskovits@gmail.com>
+# Copyright © 2017, 2018, 2019 Gábor Boskovits <boskovits@gmail.com>
 # Copyright © 2018 Amirouche Boubekki <amirouche@hypermove.net>
 # Copyright © 2018, 2019 Oleg Pykhalov <go.wigust@gmail.com>
 # Copyright © 2018 Stefan Stefanović <stefanx2ovic@gmail.com>
@@ -690,8 +690,9 @@ dist_patch_DATA =						\
   %D%/packages/patches/bazaar-CVE-2017-14176.patch		\
   %D%/packages/patches/beets-python-3.7-fix.patch		\
   %D%/packages/patches/beignet-correct-file-names.patch		\
-  %D%/packages/patches/binutils-boot-2.20.1a.patch		\
+  %D%/packages/patches/benchmark-unbundle-googletest.patch	\
   %D%/packages/patches/biber-fix-encoding-write.patch		\
+  %D%/packages/patches/binutils-boot-2.20.1a.patch		\
   %D%/packages/patches/binutils-loongson-workaround.patch	\
   %D%/packages/patches/blender-2.79-newer-ffmpeg.patch		\
   %D%/packages/patches/blender-2.79-python-3.7-fix.patch	\
@@ -739,6 +740,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/cursynth-wave-rand.patch			\
   %D%/packages/patches/cvs-2017-12836.patch			\
   %D%/packages/patches/dbus-helper-search-path.patch		\
+  %D%/packages/patches/dbus-CVE-2019-12749.patch		\
   %D%/packages/patches/dealii-mpi-deprecations.patch		\
   %D%/packages/patches/deja-dup-use-ref-keyword-for-iter.patch	\
   %D%/packages/patches/dfu-programmer-fix-libusb.patch		\
@@ -751,6 +753,8 @@ dist_patch_DATA =						\
   %D%/packages/patches/docker-use-fewer-modprobes.patch		\
   %D%/packages/patches/dovecot-trees-support-dovecot-2.3.patch	\
   %D%/packages/patches/doxygen-test.patch			\
+  %D%/packages/patches/dstat-fix-crash-when-specifying-delay.patch	\
+  %D%/packages/patches/dstat-skip-devices-without-io.patch	\
   %D%/packages/patches/dvd+rw-tools-add-include.patch 		\
   %D%/packages/patches/elfutils-tests-ptrace.patch		\
   %D%/packages/patches/elixir-path-length.patch			\
@@ -761,6 +765,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/emacs-highlight-stages-add-gexp.patch	\
   %D%/packages/patches/emacs-scheme-complete-scheme-r5rs-info.patch	\
   %D%/packages/patches/emacs-source-date-epoch.patch		\
+  %D%/packages/patches/emacs-unpackaged-req.patch		\
   %D%/packages/patches/emacs-undohist-ignored.patch	\
   %D%/packages/patches/emacs-wordnut-require-adaptive-wrap.patch	\
   %D%/packages/patches/emacs-zones-called-interactively.patch	\
@@ -937,7 +942,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/id3lib-CVE-2007-4460.patch			\
   %D%/packages/patches/idris-test-no-node.patch			\
   %D%/packages/patches/ilmbase-fix-tests.patch			\
-  %D%/packages/patches/inkscape-poppler-compat3.patch		\
   %D%/packages/patches/inkscape-poppler-0.76.patch		\
   %D%/packages/patches/intltool-perl-compatibility.patch	\
   %D%/packages/patches/irrlicht-use-system-libs.patch		\
@@ -1131,6 +1135,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/openssl-1.1-c-rehash-in.patch		\
   %D%/packages/patches/openssl-c-rehash-in.patch		\
   %D%/packages/patches/openssl-CVE-2019-1559.patch		\
+  %D%/packages/patches/open-zwave-hidapi.patch			\
   %D%/packages/patches/orpheus-cast-errors-and-includes.patch	\
   %D%/packages/patches/osip-CVE-2017-7853.patch			\
   %D%/packages/patches/ots-no-include-missing-file.patch	\
@@ -1230,6 +1235,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/randomjungle-disable-static-build.patch	\
   %D%/packages/patches/rapicorn-isnan.patch			\
   %D%/packages/patches/raptor2-heap-overflow.patch		\
+  %D%/packages/patches/ratpoints-sturm_and_rp_private.patch	\
   %D%/packages/patches/ratpoison-shell.patch			\
   %D%/packages/patches/rcs-5.9.4-noreturn.patch			\
   %D%/packages/patches/rct-add-missing-headers.patch		\
@@ -1237,6 +1243,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/readline-6.2-CVE-2014-2524.patch		\
   %D%/packages/patches/red-eclipse-remove-gamma-name-hack.patch	\
   %D%/packages/patches/reposurgeon-add-missing-docbook-files.patch	\
+  %D%/packages/patches/ri-li-modernize_cpp.patch		\
   %D%/packages/patches/ripperx-missing-file.patch		\
   %D%/packages/patches/rpcbind-CVE-2017-8779.patch		\
   %D%/packages/patches/rtags-separate-rct.patch			\
@@ -1277,6 +1284,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/sssd-curl-compat.patch			\
   %D%/packages/patches/steghide-fixes.patch			\
   %D%/packages/patches/streamlink-update-test.patch		\
+  %D%/packages/patches/stumpwm-fix-broken-read-one-line.patch	\
   %D%/packages/patches/superlu-dist-awpm-grid.patch		\
   %D%/packages/patches/superlu-dist-fix-mpi-deprecations.patch	\
   %D%/packages/patches/superlu-dist-scotchmetis.patch		\
@@ -1285,7 +1293,10 @@ dist_patch_DATA =						\
   %D%/packages/patches/swig-guile-gc.patch			\
   %D%/packages/patches/swish-e-search.patch			\
   %D%/packages/patches/swish-e-format-security.patch		\
-  %D%/packages/patches/stumpwm-fix-broken-read-one-line.patch	\
+  %D%/packages/patches/symmetrica-bruch.patch			\
+  %D%/packages/patches/symmetrica-int32.patch			\
+  %D%/packages/patches/symmetrica-return_values.patch 		\
+  %D%/packages/patches/symmetrica-sort_sum_rename.patch 	\
   %D%/packages/patches/t1lib-CVE-2010-2642.patch		\
   %D%/packages/patches/t1lib-CVE-2011-0764.patch		\
   %D%/packages/patches/t1lib-CVE-2011-1552+.patch		\
diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 9392c59521..c6ed4c6d4a 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -438,7 +438,7 @@ hostname.")
 (define-public shadow
   (package
     (name "shadow")
-    (version "4.6")
+    (version "4.7")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -446,7 +446,7 @@ hostname.")
                     "download/" version "/shadow-" version ".tar.xz"))
               (sha256
                (base32
-                "10smy01km2bqjjvsd2jz17zvrxbzj89qczyb1amk38j28bcci609"))))
+                "0v71474rx38lg9kidrm4xbk35sg3icv3s5pk2b42icp3lyj9dqg5"))))
     (build-system gnu-build-system)
     (arguments
      `(;; Assume System V `setpgrp (void)', which is the default on GNU
@@ -482,7 +482,7 @@ hostname.")
                                   "-linux")
                  `(("linux-pam" ,linux-pam))
                  '()))
-    (home-page "http://pkg-shadow.alioth.debian.org/")
+    (home-page "https://github.com/shadow-maint/shadow")
     (synopsis "Authentication-related tools such as passwd, su, and login")
     (description
      "Shadow provides a number of authentication-related tools, including:
@@ -1734,13 +1734,13 @@ of supported upstream metrics systems simultaneously.")
 (define-public ansible
   (package
     (name "ansible")
-    (version "2.8.0")
+    (version "2.8.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "ansible" version))
        (sha256
-        (base32 "1bpk5r5x6vdgn839n74yv2chd2ja10yfrhav0fzwa38mi5yxsd3j"))))
+        (base32 "0ia4x17ywym3r1m96ar4h0wc2xlylhbjp6x4wzwkh4p2i0x1vmg1"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-bcrypt" ,python-bcrypt)
@@ -2133,7 +2133,9 @@ results (ndiff), and a packet generation and response analysis tool (nping).")
              (commit (string-append "v" version))))
        (file-name (git-file-name "dstat" version))
        (sha256
-        (base32 "1qnmkhqmjd1m3if05jj29dvr5hn6kayq9bkkkh881w472c0zhp8v"))))
+        (base32 "1qnmkhqmjd1m3if05jj29dvr5hn6kayq9bkkkh881w472c0zhp8v"))
+       (patches (search-patches "dstat-fix-crash-when-specifying-delay.patch"
+                                "dstat-skip-devices-without-io.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; no make check
@@ -2142,6 +2144,11 @@ results (ndiff), and a packet generation and response analysis tool (nping).")
                             "prefix=/"))
        #:phases
        (modify-phases %standard-phases
+         (add-after 'unpack 'fix-python3-DeprecationWarning
+           (lambda _
+             (substitute* "dstat"
+               (("collections") "collections.abc"))
+             #t))
          (delete 'configure)            ; no configure script
          (add-after 'install 'wrap
            (lambda* (#:key outputs #:allow-other-keys)
@@ -2150,8 +2157,6 @@ results (ndiff), and a packet generation and response analysis tool (nping).")
                  `("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH"))))
                #t))))))
     (inputs
-     ;; Python 3 is supposedly supported but prints a DeprecationWarning.
-     ;; Upstream is dead.  See <https://github.com/dagwieers/dstat/releases>.
      `(("python" ,python-wrapper)
        ("python-six" ,python-six)))
     (synopsis "Versatile resource statistics tool")
diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 69163a43d9..561347ad98 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -43,6 +43,7 @@
   #:use-module (gnu packages mpi)
   #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages perl)
+  #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages pulseaudio)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-xyz)
@@ -92,6 +93,27 @@ multiplication routines such as Toom–Cook and the FFT.")
    (license license:lgpl3+)
    (home-page "http://mpfrcx.multiprecision.org/")))
 
+(define-public gf2x
+  (package
+   (name "gf2x")
+   (version "1.2")
+   (source (origin
+            (method url-fetch)
+            (uri (string-append
+                  "https://gforge.inria.fr/frs/download.php/file/36934/gf2x-"
+                  version ".tar.gz"))
+            (sha256
+             (base32
+              "0d6vh1mxskvv3bxl6byp7gxxw3zzpkldrxnyajhnl05m0gx7yhk1"))))
+   (build-system gnu-build-system)
+   (synopsis "Arithmetic of polynomials over binary finite fields")
+   (description
+    "The gf2x library provides arithmetic of polynomials over finite fields
+of characteristic 2.  It implements the multiplication, squaring and
+greatest common divisor operations.")
+   (license license:gpl3+)
+   (home-page "https://gforge.inria.fr/projects/gf2x/")))
+
 (define-public cm
   (package
    (name "cm")
@@ -122,24 +144,82 @@ line applications.")
 
 (define-public fplll
   (package
-   (name "fplll")
-   (version "4.0.4")
-   (source (origin
-            (method url-fetch)
-            (uri (string-append
-                  "http://perso.ens-lyon.fr/damien.stehle/fplll/libfplll-"
-                  version ".tar.gz"))
-            (sha256 (base32
-                     "1cbiby7ykis4z84swclpysrljmqhfcllpkcbll1m08rzskgb1a6b"))))
-   (build-system gnu-build-system)
-   (inputs `(("gmp" ,gmp)
-             ("mpfr" ,mpfr)))
-   (synopsis "Library for LLL-reduction of euclidean lattices")
-   (description
-    "fplll LLL-reduces euclidean lattices.  Since version 3, it can also
-solve the shortest vector problem.")
-   (license license:lgpl2.1+)
-   (home-page "http://perso.ens-lyon.fr/damien.stehle/fplll/")))
+    (name "fplll")
+    (version "5.2.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/fplll/fplll.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "015qmrd7nfaysbv1hbwiprz9g6hnww1y1z1xw8f43ysb7k1b5nbg"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)))
+    (inputs
+     `(("gmp" ,gmp)
+       ("mpfr" ,mpfr)))
+    (home-page "https://github.com/fplll/fplll")
+    (synopsis "Library for LLL-reduction of euclidean lattices")
+    (description
+     "fplll contains implementations of several lattice algorithms.
+The implementation relies on floating-point orthogonalization, and LLL
+is central to the code, hence the name.
+
+It includes implementations of floating-point LLL reduction
+algorithms, offering different speed/guarantees ratios.  It contains
+a @emph{wrapper} choosing the estimated best sequence of variants in
+order to provide a guaranteed output as fast as possible.  In the case
+of the wrapper, the succession of variants is oblivious to the user.
+
+It includes an implementation of the BKZ reduction algorithm,
+including the BKZ-2.0 improvements (extreme enumeration
+pruning, pre-processing of blocks, early termination).  Additionally,
+Slide reduction and self dual BKZ are supported.
+
+It also includes a floating-point implementation of the
+Kannan-Fincke-Pohst algorithm that finds a shortest non-zero lattice
+vector.  For the same task, the GaussSieve algorithm is also available
+in fplll.  Finally, it contains a variant of the enumeration algorithm
+that computes a lattice vector closest to a given vector belonging to
+the real span of the lattice.")
+    (license license:lgpl2.1+)))
+
+(define-public python-fpylll
+  (package
+    (name "python-fpylll")
+    (version "0.4.1")
+    (source
+     (origin
+       ;; Pypi contains and older release, so we use a tagged release from
+       ;; Github instead.
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/fplll/fpylll.git")
+             (commit (string-append version "dev"))))
+       (sha256
+        (base32
+         "01x2sqdv0sbjj4g4waj0hj4rcn4bq7h17442xaqwbznym9azmn9w"))))
+    (build-system python-build-system)
+    (inputs
+     `(("fplll" ,fplll)
+       ("gmp" ,gmp)
+       ("mpfr" ,mpfr)
+       ("pari-gp" ,pari-gp)))
+    (propagated-inputs
+     `(("cysignals" ,python-cysignals)
+       ("cython" ,python-cython)
+       ("flake8" ,python-flake8)
+       ("numpy" ,python-numpy)
+       ("pytest" ,python-pytest)))
+    (home-page "https://github.com/fplll/fpylll")
+    (synopsis "Python interface for fplll")
+    (description "fpylll is a Python wrapper for fplll.")
+    (license license:gpl2+)))
 
 (define-public pari-gp
   (package
@@ -928,7 +1008,7 @@ xtensor provides:
 (define-public gap
   (package
     (name "gap")
-    (version "4.10.0")
+    (version "4.10.1")
     (source
      (origin
        (method url-fetch)
@@ -939,7 +1019,7 @@ xtensor provides:
                            ".tar.bz2"))
        (sha256
         (base32
-         "1dmb8v4p7j1nnf7sx8sg54b49yln36bi9acwp7w1d3a1nxj17ird"))
+         "136s0zvhcw41fshj5zgsrjcy2kd58cdh2m3ddp5rdizi4rx54f10"))
        (modules '((guix build utils) (ice-9 ftw) (srfi srfi-1)))
        (snippet
         '(begin
@@ -967,20 +1047,20 @@ xtensor provides:
                    ;; Optional packages, searched for at start,
                    ;; and their depedencies.
                    "alnuth-3.1.0"
-                   "AutoDoc-2018.09.20"
                    "autpgrp-1.10"
                    "crisp-1.4.4"     ; bsd-2
-                   ; "ctbllib"       ; no explicit license, drop
+                   "ctbllib"       ; gpl3+ according to doc/chap0.txt
                    "FactInt-1.6.2"
                    "fga"
                    "irredsol-1.4"    ; bsd-2
-                   "laguna-3.9.0"
+                   "laguna-3.9.2"
                    "polenta-1.3.8"
                    "polycyclic-2.14"
                    "radiroot-2.8"
                    "resclasses-4.7.1"
                    "sophus-1.24"
-                   ; "tomlib-1.2.7"  ; no explicit license, drop
+                   "tomlib-1.2.7"  ; gpl2+, clarified in the git repository
+                                   ; and the next release
                    "utils-0.59"))))
            #t))))
     (build-system gnu-build-system)
@@ -988,7 +1068,11 @@ xtensor provides:
      `(("gmp" ,gmp)
        ("zlib" ,zlib)))
     (arguments
-     `(#:phases
+     `(#:modules ((ice-9 ftw)
+                  (srfi srfi-26)
+                  (guix build gnu-build-system)
+                  (guix build utils))
+       #:phases
        (modify-phases %standard-phases
          (add-after 'build 'build-packages
            ;; Compile all packages that have not been deleted by the
@@ -1004,19 +1088,16 @@ xtensor provides:
              (with-directory-excursion "doc"
                (invoke "./make_doc"))
              #t))
-         (replace 'check
-           (lambda _
-             ;; "make check" is expected to appear in gap-4.10.1
-             (invoke "./gap" "tst/testinstall.g")
-             #t))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
                     (bin (string-append out "/bin"))
+                    (lib (string-append out "/lib"))
                     (prog (string-append bin "/gap"))
                     (prog-real (string-append bin "/.gap-real"))
                     (share (string-append out "/share/gap"))
-                    (include (string-append out "/include/gap")))
+                    (include (string-append out "/include/gap"))
+                    (include-hpc (string-append include "/hpc")))
                ;; Install only the gap binary; the gac compiler is left
                ;; for maybe later. "Wrap" it in a shell script that calls
                ;; the binary with the correct parameter.
@@ -1030,12 +1111,37 @@ xtensor provides:
                            prog-real
                            share)))
                (chmod prog #o755)
-               ;; Install the headers and the library, which are needed by
-               ;; Sage. The Makefile targets are available in gap-4.10.0,
-               ;; but planned to be removed in gap-4.10.1.
-               (invoke "make" "install-headers")
-               (invoke "make" "install-libgap")
+               ;; Install the headers, which are needed by Sage. The
+               ;; Makefile target "install-headers" was available in
+               ;; gap-4.10.0, but has been commented out in gap-4.10.1.
+               (mkdir-p include-hpc)
                (install-file "gen/config.h" include)
+               (let ((file-name-predicate-without-stat
+                       (lambda (regex)
+                         (cut (file-name-predicate regex) <> #f))))
+                 (with-directory-excursion "src"
+                   (for-each
+                     (cut install-file <> include)
+                     (scandir "."
+                              (file-name-predicate-without-stat ".*\\.h$"))))
+                 (with-directory-excursion "src/hpc"
+                   (for-each
+                     (cut install-file <> include-hpc)
+                     (scandir "."
+                              (file-name-predicate-without-stat ".*\\.h$")))))
+               ;; Install the library, which is needed by Sage. The
+               ;; Makefile target "install-libgap" was available in
+               ;; gap-4.10.0, but has been commented out in gap-4.10.1.
+               ;; Compared to the Makefile, which used libtool, the
+               ;; following approach of copying files and making symlinks
+               ;; is rather pedestrian. There is hope that some later
+               ;; version of gap reinstates and completes the install
+               ;; targets.
+               (invoke "make" "libgap.la")
+               (install-file "libgap.la" lib)
+               (install-file ".libs/libgap.so.0.0.0" lib)
+               (symlink "libgap.so.0.0.0" (string-append lib "/libgap.so")) 
+               (symlink "libgap.so.0.0.0" (string-append lib "/libgap.so.0"))
                ;; Install a certain number of files and directories to
                ;; SHARE, where the wrapped shell script expects them.
                ;; Remove information on the build directory from sysinfo.gap.
@@ -1068,3 +1174,411 @@ objects.")
     ;; means that the gpl2+ licence of GAP itself applies, but to be on the
     ;; safe side, we drop them for now.
     (license license:gpl2+)))
+
+(define-public givaro
+  (package
+    (name "givaro")
+    (version "4.1.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/linbox-team/givaro")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "11wz57q6ijsvfs5r82masxgr319as92syi78lnl9lgdblpc6xigk"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)))
+    (propagated-inputs
+     `(("gmp" ,gmp))) ; gmp++.h includes gmpxx.h
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'bootstrap 'setenv
+           ;; Prevent the autogen.sh script to carry out the configure
+           ;; script, which has not yet been patched to replace /bin/sh.
+           (lambda _
+             (setenv "NOCONFIGURE" "yes")
+             #t)))))
+    (synopsis "Algebraic computations with exact rings and fields")
+    (description
+     "Givaro is a C++ library implementing the basic arithmetic of various
+algebraic objects: prime fields, extension fields, finite fields, finite
+rings, polynomials, algebraic numbers, arbitrary precision integers and
+rationals (C++ wrappers over gmp), fixed precision integers.  It also
+provides data-structures and templated classes for the manipulation of
+compound objects, such as vectors, matrices and univariate polynomials.")
+    (license license:cecill-b)
+    (home-page "https://github.com/linbox-team/givaro")))
+
+(define-public fflas-ffpack
+  (package
+    (name "fflas-ffpack")
+    (version "2.4.3")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/linbox-team/fflas-ffpack")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1ynbjd72qrwp0b4kpn0p5d7gddpvj8dlb5fwdxajr5pvkvi3if74"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("openblas" ,openblas)))
+    (propagated-inputs
+     `(("givaro" ,givaro))) ; required according to the .pc file
+    (arguments
+     `(#:configure-flags
+       (list (string-append "--with-blas-libs="
+                            (assoc-ref %build-inputs "openblas")
+                            "/lib/libopenblas.so"))
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'bootstrap 'setenv
+           ;; Prevent the autogen.sh script to carry out the configure
+           ;; script, which has not yet been patched to replace /bin/sh.
+           (lambda _
+             (setenv "NOCONFIGURE" "yes")
+             #t)))))
+    (synopsis "C++ library for linear algebra over finite fields")
+    (description
+     "FFLAS-FFPACK is a C++ template library for basic linear algebra
+operations over a finite field.
+FFLAS (Finite Field Linear Algebra Subprograms) provides the implementation
+of a subset of routines of the numerical BLAS; it also supports sparse
+matrix-vector products.
+FFPACK (Finite Field Linear Algebra Package) is inspired by the LAPACK
+library to provide functionalities of higher level, using the kernel
+of a BLAS.  Additionally, it provides routines specific to exact linear
+algebra, such as the row echelon form.")
+    (license license:lgpl2.1+)
+    (home-page "https://linbox-team.github.io/fflas-ffpack/")))
+
+(define-public linbox
+  (package
+    (name "linbox")
+    (version "1.6.3")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/linbox-team/linbox")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "10j6dspbsq7d2l4q3y0c1l1xwmaqqba2fxg59q5bhgk9h5d7q571"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("fflas-ffpack" ,fflas-ffpack)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'bootstrap 'setenv
+           ;; Prevent the autogen.sh script to carry out the configure
+           ;; script, which has not yet been patched to replace /bin/sh.
+           (lambda _
+             (setenv "NOCONFIGURE" "yes")
+             #t)))))
+    (synopsis "C++ library for linear algebra over exact rings")
+    (description
+     "LinBox is a C++ template library for exact linear algebra computation
+with dense, sparse, and structured matrices over the integers and over
+finite fields.")
+    (license license:lgpl2.1+)
+    (home-page "https://linbox-team.github.io/linbox/")))
+
+(define-public m4ri
+  (package
+    (name "m4ri")
+    (version "20140914")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://bitbucket.org/malb/m4ri")
+                    (commit (string-append "release-" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0xfg6pffbn8r1s0y7bn9b8i55l00d41dkmhrpf7pwk53qa3achd3"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("libpng" ,libpng)))
+    (synopsis "Arithmetic of dense matrices over F_2")
+    (description "M4RI is a library for fast arithmetic with dense matrices
+over F2.  The name M4RI comes from the first implemented algorithm: The
+Method of the Four Russians inversion algorithm published by Gregory Bard.
+This algorithm in turn is named after the Method of the Four Russians
+multiplication algorithm.")
+    (license license:gpl2+)
+    (home-page "https://bitbucket.org/malb/m4ri/")))
+
+(define-public ratpoints
+  (package
+    (name "ratpoints")
+    (version "2.1.3")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "http://www.mathe2.uni-bayreuth.de/stoll/programs/"
+                    "ratpoints-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0zhad84sfds7izyksbqjmwpfw4rvyqk63yzdjd3ysd32zss5bgf4"))
+              (patches
+               ;; Taken from
+               ;; <https://git.sagemath.org/sage.git/plain/build/pkgs/ratpoints/patches/>
+               (search-patches "ratpoints-sturm_and_rp_private.patch"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:test-target "test"
+       #:make-flags
+       (list (string-append "INSTALL_DIR=" (assoc-ref %outputs "out")))
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)            ;no configure script
+         (add-before 'install 'create-install-directories
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (mkdir-p out)
+               (with-directory-excursion out
+                 (for-each (lambda (d) (mkdir-p d))
+                           '("bin" "include" "lib"))))
+             #t)))))
+    (inputs
+     `(("gmp" ,gmp)))
+    (home-page "http://www.mathe2.uni-bayreuth.de/stoll/programs/")
+    (synopsis "Find rational points on hyperelliptic curves")
+    (description "Ratpoints tries to find all rational points within
+a given height bound on a hyperelliptic curve in a very efficient way,
+by using an optimized quadratic sieve algorithm.")
+    (license license:gpl2+)))
+
+(define-public symmetrica
+  (package
+    (name "symmetrica")
+    (version "2.0")
+    (source (origin
+              (method url-fetch/tarbomb)
+              (uri (let ((v (string-join (string-split version #\.) "_")))
+                     (string-append "http://www.algorithm.uni-bayreuth.de/"
+                                    "en/research/SYMMETRICA/"
+                                    "SYM" v "_tar.gz")))
+              (sha256
+               (base32
+                "1qhfrbd5ybb0sinl9pad64rscr08qvlfzrzmi4p4hk61xn6phlmz"))
+              ;; Taken from <https://git.sagemath.org/sage.git/plain/build/pkgs/symmetrica/patches/>
+              (patches (search-patches "symmetrica-bruch.patch"
+                                       "symmetrica-int32.patch"
+                                       "symmetrica-return_values.patch"
+                                       "symmetrica-sort_sum_rename.patch"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f                      ;no test
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-makefile
+           (lambda _
+             (substitute* "makefile"
+               (("cc -c") "gcc -c"))
+             #t))
+         (add-after 'fix-makefile 'turn-off-banner
+           (lambda _
+             (substitute* "de.c"
+               (("(INT no_banner = )FALSE" _ pre) (string-append pre "TRUE")))
+             #t))
+         (delete 'configure)            ;no configure script
+         (replace 'install              ;no install target
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (lib (string-append out "/lib"))
+                    (inc (string-append out "/include/symmetrica"))
+                    (doc (string-append out "/share/doc/symmetrica-" ,version))
+                    (static "libsymmetrica.a"))
+               ;; Build static library.
+               (apply invoke "ar" "crs" static (find-files "." "\\.o$"))
+               (invoke "ranlib" static)
+               ;; Install static library and headers.
+               (for-each (lambda (f) (install-file f inc))
+                         (find-files "." "\\.h$"))
+               (install-file "libsymmetrica.a" lib)
+               ;; Install documentation.
+               (for-each (lambda (f) (install-file f doc))
+                         (find-files "." "\\.doc$"))
+               #t))))))
+    (home-page "http://www.algorithm.uni-bayreuth.de/en/research/SYMMETRICA/")
+    (synopsis "Combinatoric C Library")
+    (description "Symmetrica is a library for combinatorics.  It has support
+for the representation theory of the symmetric group and related groups,
+combinatorics of tableaux, symmetric functions and polynomials, Schubert
+polynomials, and the representation theory of Hecke algebras of type A_n.")
+    (license license:public-domain)))
+
+(define-public m4rie
+  (package
+    (name "m4rie")
+    (version "20150908")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://bitbucket.org/malb/m4rie")
+                    (commit (string-append "release-" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0r8lv46qx5mkz5kp3ay2jnsp0mbhlqr5z2z220wdk73wdshcznss"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)))
+    (inputs
+     `(("m4ri" ,m4ri)))
+    (synopsis "Arithmetic of dense matrices over F_{2^e}")
+    (description "M4RI is a library for fast arithmetic with dense matrices
+over finite fields of characteristic 2.  So it extends the functionality
+of M4RI from F_2 to F_{2^e}.")
+    (license license:gpl2+)
+    (home-page "https://bitbucket.org/malb/m4rie/")))
+
+(define-public eclib
+  (package
+    (name "eclib")
+    (version "20190226")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/JohnCremona/eclib/")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1910np1xzyjzszay24xn4b81qhpsvhp5aix9vdpknplni2mq8kwb"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)))
+    (inputs
+     `(("gmp" ,gmp)
+       ("ntl" ,ntl)
+       ("pari-gp" ,pari-gp)))
+    (synopsis "Ranks of elliptic curves and modular symbols")
+    (description "The eclib package includes mwrank (for 2-descent on
+elliptic curves over Q) and modular symbol code; it has been written by
+John Cremona to compute his elliptic curve database.")
+    (license license:gpl2+)
+    (home-page (string-append "http://homepages.warwick.ac.uk/staff/"
+                              "J.E.Cremona/mwrank/index.html"))))
+
+(define-public lrcalc
+  (package
+    (name "lrcalc")
+    (version "1.2")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://bitbucket.org/asbuch/lrcalc")
+                    (commit (string-append "lrcalc-" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1c12d04jdyxkkav4ak8d1aqrv594gzihwhpxvc6p9js0ry1fahss"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'fix-permission
+           (lambda _
+             (chmod "lrcalc.maple.src" #o644)
+             #t)))))
+    (synopsis "Littlewood-Richardson calculator in algebraic combinatorics")
+    (description "The Littlewood-Richardson Calculator (lrcalc) is a
+program designed to compute Littlewood-Richardson coefficients.  It computes
+single Littlewood-Richardson coefficients, products of Schur functions, or
+skew Schur functions.  In addition it computes products in the small quantum
+cohomology ring of a Grassmann variety.  The software package also includes
+a program that performs fast computation of the more general multiplicative
+structure constants of Schubert polynomials.")
+    (license license:gpl2+)
+    (home-page "http://sites.math.rutgers.edu/~asbuch/lrcalc/")))
+
+(define-public iml
+  (package
+    (name "iml")
+    (version "1.0.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://www.cs.uwaterloo.ca/~astorjoh/iml-"
+                           version ".tar.bz2"))
+       (sha256
+        (base32
+         "0akwhhz9b40bz6lrfxpamp7r7wkk48p455qbn04mfnl9a1l6db8x"))))
+    (build-system gnu-build-system)
+    (inputs
+     `(("gmp", gmp)
+       ("cblas" ,openblas))) ; or any other BLAS library; the documentation
+                             ; mentions ATLAS in particular
+    (arguments
+     `(#:configure-flags
+       (list
+        (string-append "--with-gmp-include="
+                       (assoc-ref %build-inputs "gmp") "/include")
+        (string-append "--with-gmp-lib="
+                       (assoc-ref %build-inputs "gmp") "/lib")
+        "--with-cblas=-lopenblas"
+        (string-append "--with-cblas-include="
+                       (assoc-ref %build-inputs "cblas") "/include")
+        (string-append "--with-cblas-lib="
+                       (assoc-ref %build-inputs "cblas") "/lib"))))
+    (home-page "https://cs.uwaterloo.ca/~astorjoh/iml.html")
+    (synopsis
+     "Solver for systems of linear equations over the integers")
+    (description
+     "IML is a C library implementing algorithms for computing exact
+solutions to dense systems of linear equations over the integers.
+Currently, IML provides the following functionality:
+
+@itemize
+@item Nonsingular rational system solving:
+compute the unique rational solution X to the system AX=B, where A and B
+are integer matrices, A nonsingular.
+@item Compute the right nullspace or kernel of an integer matrix.
+@item Certified linear system solving:
+compute a minimal denominator solution x to a system Ax=b, where b is an
+integer vector and A is an integer matrix with arbitrary shape and
+rank profile.
+@end itemize
+
+In addition, IML provides some low level routines for a variety of mod p
+matrix operations: computing the row-echelon form, determinant, rank
+profile, and inverse of a mod p matrix. These mod p routines are not
+general purpose; they require that p satisfy some preconditions based on
+the dimension of the input matrix (usually p should be prime and should be
+no more than about 20 bits long).")
+    (license license:bsd-3)))
diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 9defc59b93..b8dbc2f00a 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -2428,17 +2428,17 @@ the Turtle syntax.")
 (define-public suil
   (package
     (name "suil")
-    (version "0.10.2")
+    (version "0.10.4")
     (source (origin
-             (method url-fetch)
-             (uri (string-append "https://download.drobilla.net/suil-"
-                                 version ".tar.bz2"))
-             (sha256
-              (base32
-               "00d43m0nai63ajb7rkm9v084jcih206y17ib3160zcvzc885ji4z"))))
+              (method url-fetch)
+              (uri (string-append "https://download.drobilla.net/suil-"
+                                  version ".tar.bz2"))
+              (sha256
+               (base32
+                "0ay7hl6nr6ip1nn9k2m8ri3b52b6sx9mhixmcy4fy3kr2a88ksd1"))))
     (build-system waf-build-system)
     (arguments
-     `(#:tests? #f        ; no check target
+     `(#:tests? #f                      ; no check target
        #:configure-flags
        '("CXXFLAGS=-std=gnu++11")))
     (inputs
@@ -3568,7 +3568,7 @@ representations.")
     (arguments
      `(#:configure-flags
        (list (string-append "PREFIX=" %output)
-             (string-append "FONT_DIR=" %output "/usr/share/consolefonts"))
+             (string-append "FONT_DIR=" %output "/share/consolefonts"))
        #:make-flags
        (let ((lib (string-append %output "/lib")))
          (list (string-append "cava_LDFLAGS = -L" lib " -Wl,-rpath " lib)))
diff --git a/gnu/packages/benchmark.scm b/gnu/packages/benchmark.scm
index 970df735aa..c513370e74 100644
--- a/gnu/packages/benchmark.scm
+++ b/gnu/packages/benchmark.scm
@@ -4,6 +4,7 @@
 ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2019 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2019 Gábor Boskovits <boskovits@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -25,7 +26,10 @@
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix git-download)
+  #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages maths)
@@ -193,3 +197,27 @@ extension to @code{time} which runs a command multiple times and prints the
 timing means, standard deviations, mins, medians, and maxes having done so.
 This can give a much better understanding of the command's performance.")
     (license license:expat)))
+
+(define-public benchmark
+  (package
+    (name "benchmark")
+    (version "1.5.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/google/benchmark.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0r9dbg4cbk47gwmayys31a83m3y67k0kh1f6pl8i869rbd609ndh"))
+              (patches (search-patches "benchmark-unbundle-googletest.patch"))))
+    (build-system cmake-build-system)
+    (native-inputs
+     `(("googletest" ,googletest)))
+    (home-page "https://github.com/google/benchmark")
+    (synopsis "Microbenchmark support library")
+    (description
+     "Benchmark is a library to benchmark code snippets,
+similar to unit tests.")
+    (license license:asl2.0)))
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e87907fac5..a1f7b2d2a8 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4467,14 +4467,14 @@ interpretation.")
 (define-public r-rhisat2
   (package
     (name "r-rhisat2")
-    (version "1.0.2")
+    (version "1.0.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rhisat2" version))
        (sha256
         (base32
-         "1y3zqvk1vbcb10r1myh6f5yzjvf7bhwhpiq78bs1k6spli4bzj0q"))))
+         "02ig9qci18n93vmya7q6bijrqsbfh69fyg8iqysf89ym2vd3x3c5"))))
     (properties `((upstream-name . "Rhisat2")))
     (build-system r-build-system)
     (native-inputs
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8dbcd5dd33..f1a73bca7e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5516,7 +5516,7 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
 (define-public ngs-sdk
   (package
     (name "ngs-sdk")
-    (version "2.9.3")
+    (version "2.9.6")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -5525,7 +5525,7 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "17c0v1nah3g3d2ib5bbi0vhma1ghd6vb9xycavqsh64lhp840rk3"))))
+                "0d5k5kabgl15as37kj9x65xc92j4gcqms86hvihw3yb6wag0r0q3"))))
     (build-system gnu-build-system)
     (arguments
      `(#:parallel-build? #f ; not supported
@@ -5582,7 +5582,7 @@ simultaneously.")
 (define-public ncbi-vdb
   (package
     (name "ncbi-vdb")
-    (version "2.9.3")
+    (version "2.9.6")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -5591,11 +5591,12 @@ simultaneously.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1l4ny67nxwv1lagk9wwjbrgm7ln7adci6dnpc7k1yaln6shj0qpm"))))
+                "0knkj1sq34hlivgv5qd6jlczqrs3ldmfgn6vbbw7p4mqxvb9mirk"))))
     (build-system gnu-build-system)
     (arguments
      `(#:parallel-build? #f ; not supported
        #:tests? #f ; no "check" target
+       #:make-flags '("HAVE_HDF5=1")
        #:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'make-files-writable
@@ -5607,6 +5608,13 @@ simultaneously.")
                      (string-append (getcwd) "/setup:"
                                     (getenv "PERL5LIB")))
              #t))
+         ;; See https://github.com/ncbi/ncbi-vdb/issues/14
+         (add-after 'unpack 'patch-krypto-flags
+           (lambda _
+             (substitute* "libs/krypto/Makefile"
+               (("-Wa,-march=generic64\\+aes") "")
+               (("-Wa,-march=generic64\\+sse4") ""))
+             #t))
          (replace 'configure
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (let ((out (assoc-ref outputs "out")))
@@ -5933,7 +5941,7 @@ sequence itself can be retrieved from these databases.")
 (define-public sra-tools
   (package
     (name "sra-tools")
-    (version "2.9.3")
+    (version "2.9.6")
     (source
      (origin
        (method git-fetch)
@@ -5943,7 +5951,7 @@ sequence itself can be retrieved from these databases.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0663gcdxkziwsmlznjxysb00621rllpbz6jwsfifq7z3dj3lwm8b"))))
+         "0vqzap68v81k0zif2mnqfy8pnw2nrhsg87p6mgq8qk3nk2jv2rgy"))))
     (build-system gnu-build-system)
     (arguments
      `(#:parallel-build? #f ; not supported
@@ -6946,14 +6954,14 @@ ungapped alignment formats.")
 (define-public r-systempiper
   (package
     (name "r-systempiper")
-    (version "1.18.0")
+    (version "1.18.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "systemPipeR" version))
        (sha256
         (base32
-         "1063vdf4g2i5xyabwvzkqfxd2j8s4zs6z4zxf8lx2ccjddhkn37a"))))
+         "1k57zyzagd7g7wl38l3cn9csylykxcllbfvyq7dz8pvihgkn0ssi"))))
     (properties `((upstream-name . "systemPipeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8548,13 +8556,13 @@ factors bound at the specific regions.")
 (define-public r-tximport
   (package
     (name "r-tximport")
-    (version "1.12.0")
+    (version "1.12.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "tximport" version))
               (sha256
                (base32
-                "0nl4imr5klwcd0xnp5y0g61d6mcgd50q60zkl86ymfmc0id368jr"))))
+                "1nq8v1sgkm2ssmvr2z3qw0zsk7zy0dzb95g1mfs8fkpjqh3nqq5s"))))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/tximport")
     (synopsis "Import and summarize transcript-level estimates for gene-level analysis")
@@ -9452,13 +9460,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
 (define-public r-seurat
   (package
     (name "r-seurat")
-    (version "3.0.1")
+    (version "3.0.2")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "Seurat" version))
               (sha256
                (base32
-                "0mx2fvhdswbcsgqxhfc6d0gr92bkibwpz2bavqdzbbxrzpdpnilc"))))
+                "016fgcmjz3sjfxdvam5hd7mdxpmpnc7f6p5zqlh97m21dgn5vpqn"))))
     (properties `((upstream-name . "Seurat")))
     (build-system r-build-system)
     (propagated-inputs
@@ -12536,15 +12544,15 @@ once.  This package provides tools to perform Drop-seq analyses.")
 (define-public pigx-rnaseq
   (package
     (name "pigx-rnaseq")
-    (version "0.0.6")
+    (version "0.0.7")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/"
-                                  "releases/download/v." version
+                                  "releases/download/v" version
                                   "/pigx_rnaseq-" version ".tar.gz"))
               (sha256
                (base32
-                "1w7cwbbz1sbvbyqh5c60iqcjfs3qsppmdgxqa1i0w5wwb9mkh27m"))))
+                "013inbh22bjvwg2w0kx5i42k66w1zl4310ldip2ax6msgprs2ydj"))))
     (build-system gnu-build-system)
     (arguments
      `(#:parallel-tests? #f             ; not supported
@@ -12559,7 +12567,9 @@ once.  This package provides tools to perform Drop-seq analyses.")
                (("^  test.sh") ""))
              #t)))))
     (inputs
-     `(("gzip" ,gzip)
+     `(("coreutils" ,coreutils)
+       ("sed" ,sed)
+       ("gzip" ,gzip)
        ("snakemake" ,snakemake)
        ("fastqc" ,fastqc)
        ("multiqc" ,multiqc)
@@ -13086,35 +13096,6 @@ known and yet unknown splice junctions.  Circular-to-linear ratios of circRNAs
 can be calculated, and a number of descriptive plots easily generated.")
     (license license:artistic2.0)))
 
-(define-public r-loomr
-  (let ((commit "df0144bd2bbceca6fadef9edc1bbc5ca672d4739")
-        (revision "1"))
-    (package
-      (name "r-loomr")
-      (version (git-version "0.2.0" revision commit))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://github.com/mojaveazure/loomR.git")
-               (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32
-           "1b1g4dlmfdyhn56bz1mkh9ymirri43wiz7rjhs7py3y7bdw1s3yr"))))
-      (build-system r-build-system)
-      (propagated-inputs
-       `(("r-r6" ,r-r6)
-         ("r-hdf5r" ,r-hdf5r)
-         ("r-iterators" ,r-iterators)
-         ("r-itertools" ,r-itertools)
-         ("r-matrix" ,r-matrix)))
-      (home-page "https://github.com/mojaveazure/loomR")
-      (synopsis "R interface for loom files")
-      (description "This package provides an R interface to access, create,
-and modify loom files.  loomR aims to be completely compatible with loompy.")
-      (license license:gpl3))))
-
 (define-public gffread
   ;; We cannot use the tagged release because it is not in sync with gclib.
   ;; See https://github.com/gpertea/gffread/issues/26
@@ -14785,3 +14766,40 @@ spliced-in} (PSI) values of alternatively-spliced exons that were computed by
 vast-tools, an RNA-Seq pipeline for alternative splicing analysis.  The plots
 are generated using @code{ggplot2}.")
     (license license:expat)))
+
+(define-public tbsp
+  (let ((commit "ec8fff4410cfb13a677dbbb95cbbc60217e64907")
+        (revision "1"))
+    (package
+      (name "tbsp")
+      (version (git-version "1.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/phoenixding/tbsp.git")
+               (commit commit)))
+         (sha256
+          (base32
+           "025ym14x8gbd6hb55lsinqj6f5qzw36i10klgs7ldzxxd7s39ki1"))))
+      (build-system python-build-system)
+      (arguments '(#:tests? #f))        ; no tests included
+      (inputs
+       `(("python-matplotlib" ,python-matplotlib)
+         ("python-networkx" ,python-networkx)
+         ("python-numpy" ,python-numpy)
+         ("python-pybigwig" ,python-pybigwig)
+         ("python-biopython" ,python-biopython)
+         ("python-scikit-learn" ,python-scikit-learn)
+         ("python-scipy" ,python-scipy)))
+      (home-page "https://github.com/phoenixding/tbsp/")
+      (synopsis "SNP-based trajectory inference")
+      (description
+       "Several studies focus on the inference of developmental and response
+trajectories from single cell RNA-Seq (scRNA-Seq) data.  A number of
+computational methods, often referred to as pseudo-time ordering, have been
+developed for this task.  CRISPR has also been used to reconstruct lineage
+trees by inserting random mutations.  The tbsp package implements an
+alternative method to detect significant, cell type specific sequence
+mutations from scRNA-Seq data.")
+      (license license:expat))))
diff --git a/gnu/packages/busybox.scm b/gnu/packages/busybox.scm
index cc6257ba35..7bb677cdd0 100644
--- a/gnu/packages/busybox.scm
+++ b/gnu/packages/busybox.scm