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gnu: randomjungle: Update homepage and sourc.
[jackhill/guix/guix.git] / gnu / packages / bioinformatics.scm
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fa572d4..782af29 100644 (file)
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -262,14 +262,14 @@ instance, it implements several methods to assess contig-wise read coverage.")
     (name "bamtools")
     (version "2.5.1")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/pezmaster31/bamtools/archive/v"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/pezmaster31/bamtools.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1z3kg24qrwq13a88n9d86izngrar4fll7gr6phddb2faw75pdgaa"))))
+                "0nfb2ypcx9959xnbz6wxh6py3xfizgmg8nrknxl95c507m9hmq8b"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f ;no "check" target
@@ -438,11 +438,11 @@ BED, GFF/GTF, VCF.")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/arq5x/bedtools2/"
-                                  "archive/v" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+                                  "releases/download/v" version
+                                  "/bedtools-" version ".tar.gz"))
               (sha256
                (base32
-                "05vrnr8yp7swfagshzpgqmzk1blnwnq8pq5pckzi1m26w98d63vf"))))
+                "11rvca19ncg03kxd0wzlfx5ws7r3nisd0z8s9j9n182d8ksp2pxz"))))
     (arguments
      '(#:test-target "test"
        #:phases
@@ -520,13 +520,14 @@ provides the Ribotaper pipeline.")
     (version "0.2.2")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/ratschlab/RiboDiff/"
-                           "archive/v" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/ratschlab/RiboDiff.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "0wpbwmfv05wdjxv7ikm664f7s7p7cqr8jnw99zrda0q67rl50aaj"))))
+         "0x75nlp7qnmm64jasbi6l21f2cy99r2cjyl6b4hr8zf2bq22drnz"))))
     (build-system python-build-system)
     (arguments
      `(#:python ,python-2
@@ -563,12 +564,14 @@ independently with transcriptional regulation.")
     (name "bioawk")
     (version "1.0")
     (source (origin
-      (method url-fetch)
-      (uri (string-append "https://github.com/lh3/bioawk/archive/v"
-                          version ".tar.gz"))
-      (file-name (string-append name "-" version ".tar.gz"))
-      (sha256
-       (base32 "1daizxsk17ahi9n58fj8vpgwyhzrzh54bzqhanjanp88kgrz7gjw"))))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/lh3/bioawk.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1pxc3zdnirxbf9a0az698hd8xdik7qkhypm7v6hn922x8y9qmspm"))))
     (build-system gnu-build-system)
     (inputs
      `(("zlib" ,zlib)))
@@ -582,13 +585,13 @@ independently with transcriptional regulation.")
        (modify-phases %standard-phases
          (delete 'configure) ; There is no configure phase.
          (replace 'install
-          (lambda* (#:key outputs #:allow-other-keys)
-            (let* ((out (assoc-ref outputs "out"))
-                   (bin  (string-append out "/bin"))
-                   (man (string-append out "/share/man/man1")))
-              (mkdir-p man)
-              (copy-file "awk.1" (string-append man "/bioawk.1"))
-              (install-file "bioawk" bin)))))))
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin  (string-append out "/bin"))
+                    (man (string-append out "/share/man/man1")))
+               (mkdir-p man)
+               (copy-file "awk.1" (string-append man "/bioawk.1"))
+               (install-file "bioawk" bin)))))))
     (home-page "https://github.com/lh3/bioawk")
     (synopsis "AWK with bioinformatics extensions")
     (description "Bioawk is an extension to Brian Kernighan's awk, adding the
@@ -688,53 +691,77 @@ Python.")
 
 (define-public python-biom-format
   (package
-   (name "python-biom-format")
-   (version "2.1.6")
-   (source
-    (origin
-     (method url-fetch)
-     ;; Use GitHub as source because PyPI distribution does not contain
-     ;; test data: https://github.com/biocore/biom-format/issues/693
-     (uri (string-append "https://github.com/biocore/biom-format/archive/"
-                         version ".tar.gz"))
-     (file-name (string-append name "-" version ".tar.gz"))
-     (sha256
-      (base32
-       "08cr7wpahk6zb31h4bs7jmzpvxcqv9s13xz40h6y2h656jvdvnpj"))))
-   (build-system python-build-system)
-   (propagated-inputs
-    `(("python-numpy" ,python-numpy)
-      ("python-scipy" ,python-scipy)
-      ("python-future" ,python-future)
-      ("python-click" ,python-click)
-      ("python-h5py" ,python-h5py)
-      ("python-pandas" ,python-pandas)))
-   (native-inputs
-    `(("python-nose" ,python-nose)))
-   (home-page "http://www.biom-format.org")
-   (synopsis "Biological Observation Matrix (BIOM) format utilities")
-   (description
-    "The BIOM file format is designed to be a general-use format for
+    (name "python-biom-format")
+    (version "2.1.7")
+    (source
+     (origin
+       (method git-fetch)
+       ;; Use GitHub as source because PyPI distribution does not contain
+       ;; test data: https://github.com/biocore/biom-format/issues/693
+       (uri (git-reference
+             (url "https://github.com/biocore/biom-format.git")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "1rna16lyk5aqhnv0dp77wwaplias93f1vw28ad3jmyw6hwkai05v"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'use-cython
+           (lambda _ (setenv "USE_CYTHON" "1") #t))
+         (add-after 'unpack 'disable-broken-test
+           (lambda _
+             (substitute* "biom/tests/test_cli/test_validate_table.py"
+               (("^(.+)def test_invalid_hdf5" m indent)
+                (string-append indent
+                               "@npt.dec.skipif(True, msg='Guix')\n"
+                               m)))
+             #t))
+         (add-before 'reset-gzip-timestamps 'make-files-writable
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (for-each (lambda (file) (chmod file #o644))
+                         (find-files out "\\.gz"))
+               #t))))))
+    (propagated-inputs
+     `(("python-numpy" ,python-numpy)
+       ("python-scipy" ,python-scipy)
+       ("python-flake8" ,python-flake8)
+       ("python-future" ,python-future)
+       ("python-click" ,python-click)
+       ("python-h5py" ,python-h5py)
+       ("python-pandas" ,python-pandas)))
+    (native-inputs
+     `(("python-cython" ,python-cython)
+       ("python-pytest" ,python-pytest)
+       ("python-pytest-cov" ,python-pytest-cov)
+       ("python-nose" ,python-nose)))
+    (home-page "http://www.biom-format.org")
+    (synopsis "Biological Observation Matrix (BIOM) format utilities")
+    (description
+     "The BIOM file format is designed to be a general-use format for
 representing counts of observations e.g. operational taxonomic units, KEGG
 orthology groups or lipid types, in one or more biological samples
 e.g. microbiome samples, genomes, metagenomes.")
-   (license license:bsd-3)
-   (properties `((python2-variant . ,(delay python2-biom-format))))))
+    (license license:bsd-3)
+    (properties `((python2-variant . ,(delay python2-biom-format))))))
 
 (define-public python2-biom-format
   (let ((base (package-with-python2 (strip-python2-variant python-biom-format))))
     (package
       (inherit base)
       (arguments
-       `(#:phases
-         (modify-phases %standard-phases
-           ;; Do not require the unmaintained pyqi library.
-           (add-after 'unpack 'remove-pyqi
-             (lambda _
-               (substitute* "setup.py"
-                 (("install_requires.append\\(\"pyqi\"\\)") "pass"))
-               #t)))
-         ,@(package-arguments base))))))
+       (substitute-keyword-arguments (package-arguments base)
+         ((#:phases phases)
+          `(modify-phases ,phases
+             ;; Do not require the unmaintained pyqi library.
+             (add-after 'unpack 'remove-pyqi
+               (lambda _
+                 (substitute* "setup.py"
+                   (("install_requires.append\\(\"pyqi\"\\)") "pass"))
+                 #t)))))))))
 
 (define-public bioperl-minimal
   (let* ((inputs `(("perl-module-build" ,perl-module-build)
@@ -2689,8 +2716,10 @@ Illumina, Roche 454, and the SOLiD platform.")
                   (string-append "  strcpy(train_dir, \"" share "/train/\");"))))
              #t))
          (replace 'build
-           (lambda _ (and (zero? (system* "make" "clean"))
-                          (zero? (system* "make" "fgs")))))
+           (lambda _
+             (invoke "make" "clean")
+             (invoke "make" "fgs")
+             #t))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (string-append (assoc-ref outputs "out")))
@@ -2707,21 +2736,24 @@ Illumina, Roche 454, and the SOLiD platform.")
              (let* ((out (string-append (assoc-ref outputs "out")))
                     (bin (string-append out "/bin/"))
                     (frag (string-append bin "run_FragGeneScan.pl")))
-               (and (zero? (system* frag ; Test complete genome.
-                             "-genome=./example/NC_000913.fna"
-                             "-out=./test2"
-                             "-complete=1"
-                             "-train=complete"))
-                    (file-exists? "test2.faa")
-                    (file-exists? "test2.ffn")
-                    (file-exists? "test2.gff")
-                    (file-exists? "test2.out")
-                    (zero? (system* ; Test incomplete sequences.
-                            frag
-                            "-genome=./example/NC_000913-fgs.ffn"
-                            "-out=out"
-                            "-complete=0"
-                            "-train=454_30")))))))))
+               ;; Test complete genome.
+               (invoke frag
+                       "-genome=./example/NC_000913.fna"
+                       "-out=./test2"
+                       "-complete=1"
+                       "-train=complete")
+               (unless (and (file-exists? "test2.faa")
+                            (file-exists? "test2.ffn")
+                            (file-exists? "test2.gff")
+                            (file-exists? "test2.out"))
+                 (error "Expected files do not exist."))
+               ;; Test incomplete sequences.
+               (invoke frag
+                       "-genome=./example/NC_000913-fgs.ffn"
+                       "-out=out"
+                       "-complete=0"
+                       "-train=454_30")
+               #t))))))
     (inputs
      `(("perl" ,perl)
        ("python" ,python-2))) ;not compatible with python 3.
@@ -2741,16 +2773,14 @@ genes in incomplete assemblies or complete genomes.")
       (version "2.3")
       (source
        (origin
-         (method url-fetch)
-         (uri (string-append
-               "https://github.com/ctSkennerton/fxtract/archive/"
-               version ".tar.gz"))
-         (file-name (string-append "ctstennerton-util-"
-                                   (string-take util-commit 7)
-                                   "-checkout"))
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/ctSkennerton/fxtract.git")
+               (commit version)))
+         (file-name (git-file-name name version))
          (sha256
           (base32
-           "0275cfdhis8517hm01is62062swmi06fxzifq7mr3knbbxjlaiwj"))))
+           "0hab3gpwf4w9s87qlbswq6ws1qqybh4dcqk79q1ahyldzai5fgp5"))))
       (build-system gnu-build-system)
       (arguments
        `(#:make-flags (list
@@ -2804,19 +2834,22 @@ comment or quality sections.")
 (define-public gemma
   (package
     (name "gemma")
-    (version "0.96")
+    (version "0.98")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/xiangzhou/GEMMA/archive/v"
-                                  version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/xiangzhou/GEMMA.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "055ynn16gd12pf78n4vr2a9jlwsbwzajpdnf2y2yilg1krfff222"))
-              (patches (search-patches "gemma-intel-compat.patch"))))
+                "1s3ncnbn45r2hh1cvrqky1kbqq6546biypr4f5mkw1kqlrgyh0yg"))))
     (inputs
-     `(("gsl" ,gsl)
+     `(("eigen" ,eigen)
+       ("gfortran" ,gfortran "lib")
+       ("gsl" ,gsl)
        ("lapack" ,lapack)
+       ("openblas" ,openblas)
        ("zlib" ,zlib)))
     (build-system gnu-build-system)
     (arguments
@@ -2831,6 +2864,15 @@ comment or quality sections.")
        #:phases
        (modify-phases %standard-phases
          (delete 'configure)
+         (add-after 'unpack 'find-eigen
+           (lambda* (#:key inputs #:allow-other-keys)
+             ;; Ensure that Eigen headers can be found
+             (setenv "CPLUS_INCLUDE_PATH"
+                     (string-append (getenv "CPLUS_INCLUDE_PATH")
+                                    ":"
+                                    (assoc-ref inputs "eigen")
+                                    "/include/eigen3"))
+             #t))
          (add-before 'build 'bin-mkdir
           (lambda _
             (mkdir-p "bin")
@@ -2854,16 +2896,16 @@ association studies (GWAS).")
 (define-public grit
   (package
     (name "grit")
-    (version "2.0.2")
+    (version "2.0.5")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/nboley/grit/archive/"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/nboley/grit.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "157in84dj70wimbind3x7sy1whs3h57qfgcnj2s6lrd38fbrb7mj"))))
+                "1l5v8vfvfbrpmgnrvbrbv40d0arhxcnmxgv2f1mlcqfa3q6bkqm9"))))
     (build-system python-build-system)
     (arguments
      `(#:python ,python-2
@@ -2875,13 +2917,7 @@ association studies (GWAS).")
              (delete-file "grit/sparsify_support_fns.c")
              (delete-file "grit/call_peaks_support_fns.c")
              (substitute* "setup.py"
-               (("Cython.Setup") "Cython.Build")
-               ;; Add numpy include path to fix compilation
-               (("pyx\", \\]")
-                (string-append "pyx\", ], include_dirs = ['"
-                               (assoc-ref inputs "python-numpy")
-                               "/lib/python2.7/site-packages/numpy/core/include/"
-                               "']")))
+               (("Cython.Setup") "Cython.Build"))
              #t)))))
     (inputs
      `(("python-scipy" ,python2-scipy)
@@ -2975,16 +3011,11 @@ particular, reads spanning multiple exons.")
     (source
      (origin
        (method url-fetch)
-       ;; FIXME: a better source URL is
-       ;; (string-append "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2"
-       ;;                "/downloads/hisat2-" version "-source.zip")
-       ;; with hash "0lywnr8kijwsc2aw10dwxic0n0yvip6fl3rjlvc8zzwahamy4x7g"
-       ;; but it is currently unavailable.
-       (uri "https://github.com/infphilo/hisat2/archive/cba6e8cb.tar.gz")
-       (file-name (string-append name "-" version ".tar.gz"))
+       (uri (string-append "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2"
+                           "/downloads/hisat2-" version "-source.zip"))
        (sha256
         (base32
-         "1mf2hdsyv7cd97xm9mp9a4qws02yrj95y6w6f6cdwnq0klp81r50"))))
+         "0lywnr8kijwsc2aw10dwxic0n0yvip6fl3rjlvc8zzwahamy4x7g"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; no check target
@@ -3091,14 +3122,14 @@ from high-throughput sequencing assays.")
     (name "java-htsjdk")
     (version "2.3.0") ; last version without build dependency on gradle
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/samtools/htsjdk/archive/"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/samtools/htsjdk.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1ibhzzxsfc38nqyk9r8zqj6blfc1kh26iirypd4q6n90hs2m6nyq"))
+                "1b178ixcabanm834ydjl3jiakpyxdmki32hqfv2abrzn3rcwa28i"))
               (modules '((guix build utils)))
               (snippet
                ;; Delete pre-built binaries
@@ -3445,26 +3476,28 @@ VCF.")
            (lambda* (#:key inputs #:allow-other-keys)
              (mkdir-p "lib/jni")
              (mkdir-p "jdk-src")
-             (and (zero? (system* "tar" "--strip-components=1" "-C" "jdk-src"
-                                  "-xf" (assoc-ref inputs "jdk-src")))
-                  (zero? (system* "javah" "-jni"
-                                  "-classpath" "classes"
-                                  "-d" "lib/"
-                                  "net.sf.samtools.util.zip.IntelDeflater"))
-                  (with-directory-excursion "src/c/inteldeflater"
-                    (zero? (system* "gcc" "-I../../../lib" "-I."
-                                    (string-append "-I" (assoc-ref inputs "jdk")
-                                                   "/include/linux")
-                                    "-I../../../jdk-src/src/share/native/common/"
-                                    "-I../../../jdk-src/src/solaris/native/common/"
-                                    "-c" "-O3" "-fPIC" "IntelDeflater.c"))
-                    (zero? (system* "gcc" "-shared"
-                                    "-o" "../../../lib/jni/libIntelDeflater.so"
-                                    "IntelDeflater.o" "-lz" "-lstdc++"))))))
+             (invoke "tar" "--strip-components=1" "-C" "jdk-src"
+                     "-xf" (assoc-ref inputs "jdk-src"))
+             (invoke "javah" "-jni"
+                     "-classpath" "classes"
+                     "-d" "lib/"
+                     "net.sf.samtools.util.zip.IntelDeflater")
+             (with-directory-excursion "src/c/inteldeflater"
+               (invoke "gcc" "-I../../../lib" "-I."
+                       (string-append "-I" (assoc-ref inputs "jdk")
+                                      "/include/linux")
+                       "-I../../../jdk-src/src/share/native/common/"
+                       "-I../../../jdk-src/src/solaris/native/common/"
+                       "-c" "-O3" "-fPIC" "IntelDeflater.c")
+               (invoke "gcc" "-shared"
+                       "-o" "../../../lib/jni/libIntelDeflater.so"
+                       "IntelDeflater.o" "-lz" "-lstdc++"))
+             #t))
          ;; We can only build everything else after building the JNI library.
          (add-after 'build-jni 'build-rest
            (lambda* (#:key make-flags #:allow-other-keys)
-             (zero? (apply system* `("ant" "all" ,@make-flags)))))
+             (apply invoke `("ant" "all" ,@make-flags))
+             #t))
          (add-before 'build 'set-JAVA6_HOME
            (lambda _
              (setenv "JAVA6_HOME" (getenv "JAVA_HOME"))
@@ -3655,14 +3688,14 @@ data.  It also provides the @command{bgzip}, @command{htsfile}, and
     (name "idr")
     (version "2.0.3")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/nboley/idr/archive/"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/nboley/idr.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1rjdly6daslw66r43g9md8znizlscn1sphycqyldzsidkc4vxqv3"))
+                "04j876h6z444v2q79drxx283d3k5snd72kj895wbalnl42206x9g"))
               ;; Delete generated C code.
               (snippet
                '(begin (delete-file "idr/inv_cdf.c") #t))))
@@ -3800,16 +3833,16 @@ data.")
 (define-public kaiju
   (package
     (name "kaiju")
-    (version "1.6.2")
+    (version "1.6.3")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/bioinformatics-centre/kaiju/archive/v"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/bioinformatics-centre/kaiju")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1kdn4rxs0kr9ibmrgrfcci71aa6j6gr71dbc8pff7731rpab6kj7"))))
+                "119pzi0ddzv9mjg4wwa6han0cwr3k3ssn7kirvsjfcq05mi5ka0x"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; There are no tests.
@@ -3823,8 +3856,7 @@ data.")
              (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
                (mkdir-p bin)
                (chdir "..")
-               (copy-recursively "bin" bin)
-               (copy-recursively "util" bin))
+               (copy-recursively "bin" bin))
              #t)))))
     (inputs
      `(("perl" ,perl)
@@ -3952,16 +3984,16 @@ sequences).")
 (define-public mash
   (package
     (name "mash")
-    (version "2.0")
+    (version "2.1")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/marbl/mash/archive/v"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/marbl/mash.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "00fx14vpmgsijwxd1xql3if934l82v8ckqgjjyyhnr36qb9qrskv"))
+                "049hwcc059p2fd9vwndn63laifvvsi0wmv84i6y1fr79k15dxwy6"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -3986,9 +4018,7 @@ sequences).")
                             "src/mash/CommandScreen.cpp")
                (("^#include \"kseq\\.h\"")
                 "#include \"htslib/kseq.h\""))
-             #t))
-         (add-after 'fix-includes 'autoconf
-           (lambda _ (zero? (system* "autoconf")))))))
+             #t)))))
     (native-inputs
      `(("autoconf" ,autoconf)
        ;; Capnproto and htslib are statically embedded in the final
@@ -4015,13 +4045,14 @@ form of assemblies or reads.")
     (version "2.12.1")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://bitbucket.org/berkeleylab/metabat/get/v"
-                           version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://bitbucket.org/berkeleylab/metabat.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "1hmvdalz3zj5sqqklg0l4npjdv37cv2hsdi1al9iby2ndxjs1b73"))
+         "0hyg2smw1nz69mfvjpk45xyyychmda92c80a0cv7baji84ri4iyn"))
        (patches (search-patches "metabat-fix-compilation.patch"))))
     (build-system scons-build-system)
     (arguments
@@ -4084,16 +4115,16 @@ probabilistic distances of genome abundance and tetranucleotide frequency.")
 (define-public minced
   (package
     (name "minced")
-    (version "0.2.0")
+    (version "0.3.2")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/ctSkennerton/minced/archive/"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/ctSkennerton/minced.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0wxmlsapxfpxfd3ps9636h7i2xy6la8i42mwh0j2lsky63h63jp1"))))
+                "1f5h9him0gd355cnx7p6pnxpknhckd4g0v62mg8zyhfbx9as25fv"))))
     (build-system gnu-build-system)
     (arguments
      `(#:test-target "test"
@@ -4205,12 +4236,13 @@ that a read originated from a particular isoform.")
          (delete 'configure)
          (replace 'check
            ;; There are no tests, so just test if it runs.
-           (lambda _ (zero? (system* "./muscle" "-version"))))
+           (lambda _ (invoke "./muscle" "-version") #t))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
                     (bin (string-append out "/bin")))
-               (install-file "muscle" bin)))))))
+               (install-file "muscle" bin)
+               #t))))))
     (home-page "http://www.drive5.com/muscle")
     (synopsis "Multiple sequence alignment program")
     (description
@@ -4235,11 +4267,6 @@ program for nucleotide and protein sequences.")
                  (base32
                   "1hkw21rq1mwf7xp0rmbb2gqc0i6p11108m69i7mr7xcjl268pxnb"))))
     (build-system gnu-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autoconf
-           (lambda _ (zero? (system* "autoreconf" "-vif")))))))
     (inputs
      ;; XXX: TODO: Enable Lua and Guile bindings.
      ;; https://github.com/tjunier/newick_utils/issues/13
@@ -4284,19 +4311,20 @@ interrupted by stop codons.  OrfM finds and prints these ORFs.")
     (license license:lgpl3+)))
 
 (define-public pplacer
-  (let ((commit "g807f6f3"))
+  (let ((commit "807f6f3"))
     (package
       (name "pplacer")
       ;; The commit should be updated with each version change.
       (version "1.1.alpha19")
       (source
        (origin
-         (method url-fetch)
-         (uri (string-append "https://github.com/matsen/pplacer/archive/v"
-                             version ".tar.gz"))
-         (file-name (string-append name "-" version ".tar.gz"))
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/matsen/pplacer.git")
+               (commit (string-append "v" version))))
+         (file-name (git-file-name name version))
          (sha256
-          (base32 "0z1lnd2s8sh6kpzg106wzbh2szw7h0hvq8syd5a6wv4rmyyz6x0f"))))
+          (base32 "11ppbbbx20p2g9wj3ff64dhnarb12q79v7qh4rk0gj6lkbz4n7cn"))))
       (build-system ocaml-build-system)
       (arguments
        `(#:ocaml ,ocaml-4.01
@@ -4313,11 +4341,12 @@ interrupted by stop codons.  OrfM finds and prints these ORFs.")
                       (local-dir "cddlib_guix"))
                  (mkdir local-dir)
                  (with-directory-excursion local-dir
-                   (system* "tar" "xvf" cddlib-src))
+                   (invoke "tar" "xvf" cddlib-src))
                  (let ((cddlib-src-folder
                         (string-append local-dir "/"
                                        (list-ref (scandir local-dir) 2)
                                        "/lib-src")))
+                   (for-each make-file-writable (find-files "cdd_src" ".*"))
                    (for-each
                     (lambda (file)
                       (copy-file file
@@ -4381,8 +4410,7 @@ downstream analysis.")
          (add-after 'unpack 'enter-scripts-dir
            (lambda _ (chdir "scripts")))
          (replace 'check
-           (lambda _
-             (zero? (system* "python" "-m" "unittest" "discover" "-v"))))
+           (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t))
          (add-after 'install 'wrap-executables
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
@@ -4642,13 +4670,14 @@ large-scale data and can be applied to hundreds of species at once.")
     (version "2.0.7")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://bitbucket.org/regulatorygenomicsupf/"
-                           "pyicoteo/get/v" version ".tar.bz2"))
-       (file-name (string-append name "-" version ".tar.bz2"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://bitbucket.org/regulatorygenomicsupf/pyicoteo.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "0d6087f29xp8wxwlj111c3sylli98n0l8ry58c51ixzq0zfm50wa"))))
+         "0hz5g8d25lbjy1wpscr490l0lmyvaix893hhax4fxnh1h9w34w8p"))))
     (build-system python-build-system)
     (arguments
      `(#:python ,python-2 ; does not work with Python 3
@@ -4679,14 +4708,14 @@ different command-line tools:
     (name "prodigal")
     (version "2.6.3")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/hyattpd/Prodigal/archive/v"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/hyattpd/Prodigal.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "17srxkqd3jc77xk15pfbgg1a9xahqg7337w95mrsia7mpza4l2c9"))))
+                "1fs1hqk83qjbjhrvhw6ni75zakx5ki1ayy3v6wwkn3xvahc9hi5s"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ;no check target
@@ -4732,10 +4761,11 @@ partial genes, and identifies translation initiation sites.")
                                            (getenv "PATH")))
              (setenv "PERL5LIB" (string-append (getcwd) "/lib" ":"
                                                (getenv "PERL5LIB")))
-             (zero? (length (filter (lambda (file)
-                                      (display file)(display "\n")
-                                      (not (zero? (system* "perl" file))))
-                                    (find-files "t" ".*\\.t$"))))))
+             (for-each (lambda (file)
+                         (display file)(display "\n")
+                         (invoke "perl" file))
+                       (find-files "t" ".*\\.t$"))
+             #t))
          (replace 'install
            ;; There is no 'install' target in the Makefile.
            (lambda* (#:key outputs #:allow-other-keys)
@@ -4824,18 +4854,17 @@ extremely diverse sets of genomes.")
 (define-public raxml
   (package
     (name "raxml")
-    (version "8.2.10")
+    (version "8.2.12")
     (source
      (origin
-       (method url-fetch)
-       (uri
-        (string-append
-         "https://github.com/stamatak/standard-RAxML/archive/v"
-         version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/stamatak/standard-RAxML.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "13s7aspfdcfr6asynwdg1x6vznys6pzap5f8wsffbnnwpkkg9ya8"))))
+         "1jqjzhch0rips0vp04prvb8vmc20c5pdmsqn8knadcf91yy859fh"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; There are no tests.
@@ -5028,21 +5057,24 @@ distribution, coverage uniformity, strand specificity, etc.")
            (modify-phases %standard-phases
              (replace 'bootstrap
                (lambda _
-                 (invoke "bash" "gen_auto")))
+                 (substitute* "gen_tools_am"
+                   (("/usr/bin/env.*") (which "perl")))
+                 (invoke "bash" "gen_auto")
+                 #t))
              (add-after 'build 'build-additional-tools
                (lambda* (#:key make-flags #:allow-other-keys)
-                 (every (lambda (dir)
-                          (with-directory-excursion (string-append "tools/" dir)
-                            (zero? (apply system* "make" make-flags))))
-                        dirs)))
+                 (for-each (lambda (dir)
+                             (with-directory-excursion (string-append "tools/" dir)
+                               (apply invoke "make" make-flags)))
+                           dirs)
+                 #t))
              (add-after 'install 'install-additional-tools
                (lambda* (#:key make-flags #:allow-other-keys)
-                 (fold (lambda (dir result)
-                         (with-directory-excursion (string-append "tools/" dir)
-                           (and result
-                                (zero? (apply system*
-                                              `("make" ,@make-flags "install"))))))
-                       #t dirs)))))))
+                 (for-each (lambda (dir)
+                             (with-directory-excursion (string-append "tools/" dir)
+                               (apply invoke `("make" ,@make-flags "install"))))
+                           dirs)
+                 #t))))))
       (inputs
        `(("gsl" ,gsl)
          ("boost" ,boost)
@@ -5208,17 +5240,16 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
 (define-public ngs-sdk
   (package
     (name "ngs-sdk")
-    (version "1.3.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri
-        (string-append "https://github.com/ncbi/ngs/archive/"
-                       version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
-       (sha256
-        (base32
-         "1wiyf4c6nm2j87pv015cbi0qny5byf3pbvcw3likifz5dl56ag40"))))
+    (version "2.9.3")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/ncbi/ngs.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "17c0v1nah3g3d2ib5bbi0vhma1ghd6vb9xycavqsh64lhp840rk3"))))
     (build-system gnu-build-system)
     (arguments
      `(#:parallel-build? #f ; not supported
@@ -5234,9 +5265,10 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
 
                ;; The 'configure' script doesn't recognize things like
                ;; '--enable-fast-install'.
-               (zero? (system* "./configure"
-                               (string-append "--build-prefix=" (getcwd) "/build")
-                               (string-append "--prefix=" out))))))
+               (invoke "./configure"
+                       (string-append "--build-prefix=" (getcwd) "/build")
+                       (string-append "--prefix=" out))
+               #t)))
          (add-after 'unpack 'enter-dir
            (lambda _ (chdir "ngs-sdk") #t)))))
     (native-inputs `(("perl" ,perl)))
@@ -5274,23 +5306,24 @@ simultaneously.")
 (define-public ncbi-vdb
   (package
     (name "ncbi-vdb")
-    (version "2.8.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri
-        (string-append "https://github.com/ncbi/ncbi-vdb/archive/"
-                       version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
-       (sha256
-        (base32
-         "1acn4bv81mfl137qnbn9995mjjhwd36pm0b7qli1iw5skrxa9j8m"))))
+    (version "2.9.3")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/ncbi/ncbi-vdb.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1l4ny67nxwv1lagk9wwjbrgm7ln7adci6dnpc7k1yaln6shj0qpm"))))
     (build-system gnu-build-system)
     (arguments
      `(#:parallel-build? #f ; not supported
        #:tests? #f ; no "check" target
        #:phases
        (modify-phases %standard-phases
+         (add-after 'unpack 'make-files-writable
+           (lambda _ (for-each make-file-writable (find-files "." ".*")) #t))
          (add-before 'configure 'set-perl-search-path
            (lambda _
              ;; Work around "dotless @INC" build failure.
@@ -5324,8 +5357,7 @@ simultaneously.")
 
                ;; The 'configure' script doesn't recognize things like
                ;; '--enable-fast-install'.
-               (zero? (system*
-                       "./configure"
+               (invoke "./configure"
                        (string-append "--build-prefix=" (getcwd) "/build")
                        (string-append "--prefix=" (assoc-ref outputs "out"))
                        (string-append "--debug")
@@ -5334,7 +5366,8 @@ simultaneously.")
                        (string-append "--with-ngs-sdk-prefix="
                                       (assoc-ref inputs "ngs-sdk"))
                        (string-append "--with-hdf5-prefix="
-                                      (assoc-ref inputs "hdf5")))))))
+                                      (assoc-ref inputs "hdf5")))
+               #t)))
          (add-after 'install 'install-interfaces
            (lambda* (#:key outputs #:allow-other-keys)
              ;; Install interface libraries.  On i686 the interface libraries
@@ -5439,12 +5472,13 @@ subsequent visualization, annotation and storage of results.")
     (version "1.90b4")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/chrchang/plink-ng/archive/v"
-                           version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/chrchang/plink-ng.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "09ixrds009aczjswxr2alcb774mksq5g0v78dgjjn1h4dky0kf9a"))))
+        (base32 "02npdwgkpfkdnhw819rhj5kw02a5k5m90b14zq9zzya4hyg929c0"))))
     (build-system gnu-build-system)
     (arguments
      '(#:tests? #f ;no "check" target
@@ -5526,14 +5560,14 @@ structures, classes for genomic regions, mapped sequencing reads, etc.")
 (define-public preseq
   (package
     (name "preseq")
-    (version "2.0")
+    (version "2.0.3")
     (source (origin
               (method url-fetch)
-              (uri (string-append "https://github.com/smithlabcode/"
-                                  "preseq/archive/v" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (uri (string-append "https://github.com/smithlabcode/preseq/"
+                                  "releases/download/v" version
+                                  "/preseq_v" version ".tar.bz2"))
               (sha256
-               (base32 "08r684l50pnxjpvmhzjgqq56yv9rfw90k8vx0nsrnrzk8mf9hsdq"))
+               (base32 "149x9xmk1wy1gff85325yfzqc0qk4sgp1w6gbyj9cnji4x1dszbl"))
               (modules '((guix build utils)))
               (snippet '(begin
                           ;; Remove bundled samtools.
@@ -5623,17 +5657,17 @@ sequence itself can be retrieved from these databases.")
 (define-public sra-tools
   (package
     (name "sra-tools")
-    (version "2.8.2-1")
+    (version "2.9.3")
     (source
      (origin
-       (method url-fetch)
-       (uri
-        (string-append "https://github.com/ncbi/sra-tools/archive/"
-                       version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/ncbi/sra-tools.git")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "1camsijmvv2s45mb4iyf44ghl4gkd4rl0viphpcgl3ccchy32a0g"))))
+         "0663gcdxkziwsmlznjxysb00621rllpbz6jwsfifq7z3dj3lwm8b"))))
     (build-system gnu-build-system)
     (arguments
      `(#:parallel-build? #f ; not supported
@@ -5683,8 +5717,7 @@ sequence itself can be retrieved from these databases.")
 
              ;; The 'configure' script doesn't recognize things like
              ;; '--enable-fast-install'.
-             (zero? (system*
-                     "./configure"
+             (invoke "./configure"
                      (string-append "--build-prefix=" (getcwd) "/build")
                      (string-append "--prefix=" (assoc-ref outputs "out"))
                      (string-append "--debug")
@@ -5702,18 +5735,7 @@ sequence itself can be retrieved from these databases.")
                      (string-append "--with-ngs-sdk-prefix="
                                     (assoc-ref inputs "ngs-sdk"))
                      (string-append "--with-hdf5-prefix="
-                                    (assoc-ref inputs "hdf5"))))))
-         ;; This version of sra-tools fails to build with glibc because of a
-         ;; naming conflict.  glibc-2.25/include/bits/mathcalls.h already
-         ;; contains a definition of "canonicalize", so we rename it.
-         ;;
-         ;; See upstream bug report:
-         ;; https://github.com/ncbi/sra-tools/issues/67
-         (add-after 'unpack 'patch-away-glibc-conflict
-           (lambda _
-             (substitute* "tools/bam-loader/bam.c"
-               (("canonicalize\\(" line)
-                (string-append "sra_tools_" line)))
+                                    (assoc-ref inputs "hdf5")))
              #t)))))
     (native-inputs `(("perl" ,perl)))
     (inputs
@@ -5840,24 +5862,16 @@ is one that takes arguments.")
 (define-public seqtk
   (package
     (name "seqtk")
-    (version "1.2")
+    (version "1.3")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/lh3/seqtk/archive/v"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/lh3/seqtk.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0ywdyzpmfiz2wp6ampbzqg4y8bj450nfgqarpamg045b8mk32lxx"))
-                            (modules '((guix build utils)))
-              (snippet
-               '(begin
-                  ;; Remove extraneous header files, as is done in the seqtk
-                  ;; master branch.
-                  (for-each (lambda (file) (delete-file file))
-                            (list "ksort.h" "kstring.h" "kvec.h"))
-                  #t))))
+                "1bfzlqa84b5s1qi22blmmw2s8xdyp9h9ydcq22pfjhh5gab3yz6l"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -5865,11 +5879,12 @@ is one that takes arguments.")
          (delete 'configure)
          (replace 'check
            ;; There are no tests, so we just run a sanity check.
-           (lambda _ (zero? (system* "./seqtk" "seq"))))
+           (lambda _ (invoke "./seqtk" "seq") #t))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
-               (install-file "seqtk" bin)))))))
+               (install-file "seqtk" bin)
+               #t))))))
     (inputs
      `(("zlib" ,zlib)))
     (home-page "https://github.com/lh3/seqtk")
@@ -5885,20 +5900,20 @@ optionally compressed by gzip.")
     (name "snap-aligner")
     (version "1.0beta.18")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/amplab/snap/archive/v"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/amplab/snap.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1vnsjwv007k1fl1q7d681kbwn6bc66cgw6h16hym6gvyy71qv2ly"))))
+                "01w3qq4wm07z73vky0cfwlmrbf50n3w722cxrlzxfi99mnb808d8"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases
        (modify-phases %standard-phases
          (delete 'configure)
-         (replace 'check (lambda _ (zero? (system* "./unit_tests"))))
+         (replace 'check (lambda _ (invoke "./unit_tests") #t))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
@@ -5927,14 +5942,14 @@ of these reads to align data quickly through a hash-based indexing scheme.")
     (version "2.1b")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append
-             "https://github.com/biocore/sortmerna/archive/"
-             version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/biocore/sortmerna.git")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "1ghaghvd82af9j5adavxh77g7hm247d1r69m3fbi6f1jdivj5ldk"))))
+         "0j3mbz4n25738yijmjbr5r4fyvkgm8v5vn3sshyfvmyqf5q9byqf"))))
     (build-system gnu-build-system)
     (outputs '("out"      ;for binaries
                "db"))     ;for sequence databases
@@ -6180,8 +6195,7 @@ Cuffdiff or Ballgown programs.")
        #:phases
        (modify-phases %standard-phases
          (replace 'check
-           (lambda _
-             (zero? (system* "python" "-m" "unittest" "discover" "-v")))))))
+           (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t)))))
     (propagated-inputs
      `(("python-sqlalchemy" ,python2-sqlalchemy)
        ("python-decorator" ,python2-decorator)
@@ -6814,17 +6828,17 @@ SELECT or UPDATE queries to an end-point.")
 (define-public vsearch
   (package
     (name "vsearch")
-    (version "2.8.0")
+    (version "2.9.1")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append
-             "https://github.com/torognes/vsearch/archive/v"
-             version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/torognes/vsearch.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "15pbirgzhvflj4pi5n82vybbzjy9mlb0lv5l3qhrmdkfzpbyahw3"))
+         "0vhrpjfdf75ba04b24xknp41790cvcgwl0vgpy7qbzj5xh2521ss"))
        (patches (search-patches "vsearch-unbundle-cityhash.patch"))
        (snippet
         '(begin
@@ -6835,11 +6849,6 @@ SELECT or UPDATE queries to an end-point.")
            (delete-file "src/city.cc")
            #t))))
     (build-system gnu-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autogen
-           (lambda _ (zero? (system* "autoreconf" "-vif")))))))
     (inputs
      `(("zlib" ,zlib)
        ("bzip2" ,bzip2)
@@ -7090,13 +7099,13 @@ Bioconductor, CRAN, and Github.")
 (define-public r-biocviews
   (package
     (name "r-biocviews")
-    (version "1.50.1")
+    (version "1.50.5")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biocViews" version))
               (sha256
                (base32
-                "0hjm3r58i0r9qhyar9pk250cx7sfijg0lnvi12a9s6brmmbip1a3"))))
+                "0rc1n89n04ylvy9gvsgvizcs77bh70jg1nkjjsjs7rqbr3zzdysz"))))
     (properties
      `((upstream-name . "biocViews")))
     (build-system r-build-system)
@@ -7259,13 +7268,13 @@ abnormal copy number.")
 (define-public r-s4vectors
   (package
     (name "r-s4vectors")
-    (version "0.20.0")
+    (version "0.20.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "S4Vectors" version))
               (sha256
                (base32
-                "0qgiykjhnsvvpcp3zwmrnpx3bv3msvj0szchyvb1yb0fxw716xc5"))))
+                "18whrw67nxn82xshckl2pjy7d14sa3c27h3n9naqyqwz88lr6dzg"))))
     (properties
      `((upstream-name . "S4Vectors")))
     (build-system r-build-system)
@@ -7340,7 +7349,7 @@ possible.")
 (define-public r-genomeinfodbdata
   (package
     (name "r-genomeinfodbdata")
-    (version "1.1.0")
+    (version "1.2.0")
     (source (origin
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
@@ -7350,7 +7359,7 @@ possible.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0k1hsjx6n2i1sf14hyrgdhxqxm5mxk0bgnivhiax944whcicmzbf"))))
+                "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c"))))
     (properties
      `((upstream-name . "GenomeInfoDbData")))
     (build-system r-build-system)
@@ -7363,13 +7372,13 @@ ID and species.  It is used by functions in the GenomeInfoDb package.")
 (define-public r-genomeinfodb
   (package
     (name "r-genomeinfodb")
-    (version "1.18.0")
+    (version "1.18.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomeInfoDb" version))
               (sha256
                (base32
-                "1xqpgngd8by0yn627v9kz26a03v5a1lhcfwlnx2i0ivplk9bd40s"))))
+                "049pyzr8iszv3g7wdqf3pz7vg7bzd450c20ln6fgw4g5xnkkr10s"))))
     (properties
      `((upstream-name . "GenomeInfoDb")))
     (build-system r-build-system)
@@ -7648,13 +7657,13 @@ objects.")
 (define-public r-biostrings
   (package
     (name "r-biostrings")
-    (version "2.50.0")
+    (version "2.50.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Biostrings" version))
               (sha256
                (base32
-                "0zw0dj67fnpbz4iqnam5fxs92c1c8w8d7mzl0rkq4ksx0xl8vgg7"))))
+                "1qyv1ps7vy6gy78pm2rcikg0bgf1mv7falahjp3pkwqq1272hrl8"))))
     (properties
      `((upstream-name . "Biostrings")))
     (build-system r-build-system)
@@ -7901,7 +7910,7 @@ extracting the desired features in a convenient format.")
 (define-public r-go-db
   (package
     (name "r-go-db")
-    (version "3.6.0")
+    (version "3.7.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.bioconductor.org/packages/"
@@ -7909,7 +7918,7 @@ extracting the desired features in a convenient format.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0fi2qywr9apg5lwfqfq9qq6bgrnv4rdhxx25656qn4bsy62i838j"))))
+                "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5"))))
     (properties
      `((upstream-name . "GO.db")))
     (build-system r-build-system)
@@ -8112,7 +8121,7 @@ genomic intervals.  In addition, it can use BAM or BigWig files as input.")
 (define-public r-genomationdata
   (package
     (name "r-genomationdata")
-    (version "1.10.0")
+    (version "1.14.0")
     (source (origin
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
@@ -8122,7 +8131,7 @@ genomic intervals.  In addition, it can use BAM or BigWig files as input.")
                                   "genomationData_" version ".tar.gz"))
               (sha256
                (base32
-                "0h7g5x3kyb50qlblz5hc85lfm6n6f5nb68i146way3ggs04sqvla"))))
+                "10xyb8akjrhmak2i0mnv1agny2ipy364q9nlibyplpzc7vdb6bw7"))))
     (build-system r-build-system)
     ;; As this package provides little more than large data files, it doesn't
     ;; make sense to build substitutes.
@@ -8140,7 +8149,7 @@ downloaded from Encode.")
 (define-public r-org-hs-eg-db
   (package
     (name "r-org-hs-eg-db")
-    (version "3.5.0")
+    (version "3.7.0")
     (source (origin
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
@@ -8150,7 +8159,7 @@ downloaded from Encode.")
                                   "org.Hs.eg.db_" version ".tar.gz"))
               (sha256
                (base32
-                "1v6wa5613cjq59xd7x1qz8lr9nb2abm9abl2cci1khrnrlpla927"))))
+                "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
     (properties
      `((upstream-name . "org.Hs.eg.db")))
     (build-system r-build-system)
@@ -8166,7 +8175,7 @@ on mapping using Entrez Gene identifiers.")
 (define-public r-org-ce-eg-db
   (package
     (name "r-org-ce-eg-db")
-    (version "3.5.0")
+    (version "3.7.0")
     (source (origin
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
@@ -8176,7 +8185,7 @@ on mapping using Entrez Gene identifiers.")
                                   "org.Ce.eg.db_" version ".tar.gz"))
               (sha256
                (base32
-                "02ggchixlmzywhsbr0h2ms4dravv7m5964cjxqcjxqs16vjwlbk9"))))
+                "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
     (properties
      `((upstream-name . "org.Ce.eg.db")))
     (build-system r-build-system)
@@ -8192,7 +8201,7 @@ annotations for the genome of the model worm Caenorhabditis elegans.")
 (define-public r-org-dm-eg-db
   (package
     (name "r-org-dm-eg-db")
-    (version "3.5.0")
+    (version "3.7.0")
     (source (origin
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
@@ -8202,7 +8211,7 @@ annotations for the genome of the model worm Caenorhabditis elegans.")
                                   "org.Dm.eg.db_" version ".tar.gz"))
               (sha256
                (base32
-                "033qak1d3wwz17va0bh8z8p8arx0aw2va6gm1qfwsvdkj9cd9d7d"))))
+                "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
     (properties
      `((upstream-name . "org.Dm.eg.db")))
     (build-system r-build-system)
@@ -8218,7 +8227,7 @@ annotations for the genome of the model fruit fly Drosophila melanogaster.")
 (define-public r-org-mm-eg-db
   (package
     (name "r-org-mm-eg-db")
-    (version "3.5.0")
+    (version "3.7.0")
     (source (origin
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
@@ -8228,7 +8237,7 @@ annotations for the genome of the model fruit fly Drosophila melanogaster.")
                                   "org.Mm.eg.db_" version ".tar.gz"))
               (sha256
                (base32
-                "11q21p3ki4bn4hb3aix0g775l45l66jmas6m94nfhqqnpjhv4d6g"))))
+                "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
     (properties
      `((upstream-name . "org.Mm.eg.db")))
     (build-system r-build-system)
@@ -8359,7 +8368,7 @@ in Biostrings objects.")
 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
   (package
     (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
-    (version "3.4.0")
+    (version "3.4.4")
     (source (origin
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
@@ -8370,7 +8379,7 @@ in Biostrings objects.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "08gava9wsvpcqz51k2sni3pj03n5155v32d9riqbf305nbirqbkb"))))
+                "01lgxc1fx5nhlpbwjd5zqghkkbmh6axd98ikx4b0spv0jdg6gf39"))))
     (properties
      `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
     (build-system r-build-system)
@@ -8641,41 +8650,33 @@ paired-end data.")
 (define-public r-rcas
   (package
     (name "r-rcas")
-    (version "1.6.0")
+    (version "1.8.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "RCAS" version))
               (sha256
                (base32
-                "0vmn7a0rm2ban0kaxrf5danhss2r4hfhnwh5889fjcgqy300fdd5"))))
+                "0ss5hcg2m7gjji6dd23zxa5bd5a7knwcnada4qs5q2l4clgk39ad"))))
     (build-system r-build-system)
-    (native-inputs
-     `(("r-testthat" ,r-testthat)
-       ;; During vignette building knitr checks that "pandoc-citeproc"
-       ;; is in the PATH.
-       ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)))
     (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biocgenerics" ,r-biocgenerics)
        ("r-biomart" ,r-biomart)
        ("r-biostrings" ,r-biostrings)
        ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
-       ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
-       ("r-bsgenome-celegans-ucsc-ce10" ,r-bsgenome-celegans-ucsc-ce10)
-       ("r-bsgenome-dmelanogaster-ucsc-dm3" ,r-bsgenome-dmelanogaster-ucsc-dm3)
        ("r-cowplot" ,r-cowplot)
        ("r-data-table" ,r-data-table)
        ("r-dbi" ,r-dbi)
        ("r-dt" ,r-dt)
        ("r-genomation" ,r-genomation)
+       ("r-genomeinfodb" ,r-genomeinfodb)
        ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
        ("r-ggplot2" ,r-ggplot2)
        ("r-ggseqlogo" ,r-ggseqlogo)
        ("r-knitr" ,r-knitr)
        ("r-motifrg" ,r-motifrg)
        ("r-org-hs-eg-db" ,r-org-hs-eg-db)
-       ("r-org-ce-eg-db" ,r-org-ce-eg-db)
-       ("r-org-dm-eg-db" ,r-org-dm-eg-db)
-       ("r-org-mm-eg-db" ,r-org-mm-eg-db)
        ("r-pbapply" ,r-pbapply)
        ("r-pheatmap" ,r-pheatmap)
        ("r-plotly" ,r-plotly)
@@ -8857,13 +8858,14 @@ Sequences.")
     (version "1.1.4")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/ManuSetty/SeqGL/"
-                           "archive/" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/ManuSetty/SeqGL.git")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "0pnk1p3sci5yipyc8xnb6jbmydpl80fld927xgnbcv104hy8h8yh"))))
+         "1r6ywvhxl3ffv48lgj7sbd582mcc6dha3ksgc2qjlvjrnkbj3799"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biostrings" ,r-biostrings)
@@ -8939,13 +8941,13 @@ of gene-level counts.")
 (define-public r-rhdf5
   (package
     (name "r-rhdf5")
-    (version "2.24.0")
+    (version "2.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rhdf5" version))
               (sha256
                (base32
-                "15cmmchhk8bnp94gxg0zk9qyzdjx5kv16dzpbnb62mkq7ydmifx6"))))
+                "0xmpkfdsmgl79ffffj7cf9fx3zxki2rk0xn25k778kr3s0sbmhis"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rhdf5lib" ,r-rhdf5lib)))
@@ -9025,7 +9027,7 @@ AM_CONDITIONAL(AMPNG, true)"))
                (("\\$\\(bindir\\)/embossupdate") ""))
              #t))
          (add-after 'disable-update-check 'autogen
-           (lambda _ (zero? (system* "autoreconf" "-vif")))))))
+           (lambda _ (invoke "autoreconf" "-vif") #t)))))
     (inputs
      `(("perl" ,perl)
        ("libpng" ,libpng)
@@ -9198,12 +9200,14 @@ group or two ChIP groups run under different conditions.")
       (name "filevercmp")
       (version (string-append "0-1." (string-take commit 7)))
       (source (origin
-        (method url-fetch)
-        (uri (string-append "https://github.com/ekg/filevercmp/archive/"
-                            commit ".tar.gz"))
-        (file-name (string-append name "-" version ".tar.gz"))
-        (sha256
-         (base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450"))))
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/ekg/filevercmp.git")
+                      (commit commit)))
+                (file-name (git-file-name name commit))
+                (sha256
+                 (base32
+                  "1j9vxsy0y050v59h0q1d6501fcw1kjvj0d18l1xk2zyg0jzj247c"))))
       (build-system gnu-build-system)
       (arguments
        `(#:tests? #f ; There are no tests to run.
@@ -9213,7 +9217,8 @@ group or two ChIP groups run under different conditions.")
            (replace 'install
              (lambda* (#:key outputs #:allow-other-keys)
                (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
-                 (install-file "filevercmp" bin)))))))
+                 (install-file "filevercmp" bin)
+                 #t))))))
       (home-page "https://github.com/ekg/filevercmp")
       (synopsis "This program compares version strings")
       (description "This program compares version strings.  It intends to be a
@@ -9537,14 +9542,14 @@ proteomics packages.")
 (define-public r-mzr
   (package
     (name "r-mzr")
-    (version "2.14.0")
+    (version "2.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mzR" version))
        (sha256
         (base32
-         "190m2bq5bqxhljaj4f7vz9wj5h5laaxd8zp5jampnql6xc4zmarg"))
+         "0li1y6p95ljiva4lvfmql9sipn4dq42sknbh60b36ycjppnf8lj5"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -9566,11 +9571,11 @@ proteomics packages.")
              #t)))))
     (inputs
      `(("boost" ,boost) ; use this instead of the bundled boost sources
-       ("netcdf" ,netcdf)
        ("zlib" ,zlib)))
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
        ("r-biocgenerics" ,r-biocgenerics)
+       ("r-ncdf4" ,r-ncdf4)
        ("r-protgenerics" ,r-protgenerics)
        ("r-rcpp" ,r-rcpp)
        ("r-rhdf5lib" ,r-rhdf5lib)
@@ -9735,14 +9740,14 @@ structure (pcaRes) to provide a common interface to the PCA results.")
 (define-public r-msnbase
   (package
     (name "r-msnbase")
-    (version "2.8.0")
+    (version "2.8.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MSnbase" version))
        (sha256
         (base32
-         "0nnlydpklmv9kwlk3gkjgabx7l6y4gav3imq98w8wskb1fhm50c0"))))
+         "0y658anh06vnvbkfs7r8q40gqgyqr2r8kj7jlpnp33fy1lvp1nv7"))))
     (properties `((upstream-name . "MSnbase")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10210,14 +10215,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
 (define-public r-ensembldb
   (package
     (name "r-ensembldb")
-    (version "2.6.0")
+    (version "2.6.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ensembldb" version))
        (sha256
         (base32
-         "12jqz9h6w4mxyfr43w5qbwmacn512aw0mnl0zvhsg5i7p4qj45ks"))))
+         "0hdz1f34v7sas2v4225icwl3wd4sf17ykpd5dkbx1hc7wcy4w3np"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -10812,14 +10817,14 @@ problems in genomics, brain imaging, astrophysics, and data mining.")
 (define-public r-hdf5array
   (package
     (name "r-hdf5array")
-    (version "1.8.1")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "HDF5Array" version))
        (sha256
         (base32
-         "1s44zgm9jg82bk4b8k3dh7xw7mxychlfm3grs8516mxnw91zpvy5"))))
+         "1w7ad8cfsbh5xx82m3l4lc0vbmj9lcsqxxpiy3ana2ycgn1bqv3g"))))
     (properties `((upstream-name . "HDF5Array")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10838,14 +10843,20 @@ block processing.")
 (define-public r-rhdf5lib
   (package
     (name "r-rhdf5lib")
-    (version "1.2.1")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rhdf5lib" version))
        (sha256
         (base32
-         "1y59acac6v8hrhv84gghn9ifsni9xxxacaj177rrl4frmkrz4x3c"))))
+         "01gpz780g850ql20b2ql6pvr678ydk4nq4sn5iiih94a4crb9lz1"))
+       (modules '((guix build utils)))
+       (snippet
+        '(begin
+           ;; Delete bundled binaries
+           (delete-file-recursively "src/winlib/")
+           #t))))
     (properties `((upstream-name . "Rhdf5lib")))
     (build-system r-build-system)
     (arguments
@@ -10862,7 +10873,7 @@ block processing.")
                 "'%s/libhdf5.a %s/libhdf5.a -lz'"))
              (with-directory-excursion "src"
                (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
-               (rename-file (string-append "hdf5-" ,(package-version hdf5))
+               (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
                             "hdf5")
                ;; Remove timestamp and host system information to make
                ;; the build reproducible.
@@ -10891,9 +10902,9 @@ block processing.")
     (inputs
      `(("zlib" ,zlib)))
     (propagated-inputs
-     `(("hdf5" ,hdf5)))
+     `(("hdf5" ,hdf5-1.10)))
     (native-inputs
-     `(("hdf5-source" ,(package-source hdf5))))
+     `(("hdf5-source" ,(package-source hdf5-1.10))))
     (home-page "https://bioconductor.org/packages/Rhdf5lib")
     (synopsis "HDF5 library as an R package")
     (description "This package provides C and C++ HDF5 libraries for use in R
@@ -11034,19 +11045,21 @@ variable and significantly correlated genes.")
 (define-public r-delayedmatrixstats
   (package
     (name "r-delayedmatrixstats")
-    (version "1.2.0")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DelayedMatrixStats" version))
        (sha256
         (base32
-         "1dasghfy8x27zzmd0igag4mc1gxxxbchsl4hpc1050dj3wnw9w3y"))))
+         "03fk2avl1vyjv2wslczkc82qr0zmp1ra8iimd47pbmnnm839ly4w"))))
     (properties
      `((upstream-name . "DelayedMatrixStats")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-delayedarray" ,r-delayedarray)
+     `(("r-biocparallel" ,r-biocparallel)
+       ("r-delayedarray" ,r-delayedarray)
+       ("r-hdf5array" ,r-hdf5array)
        ("r-iranges" ,r-iranges)
        ("r-matrix" ,r-matrix)
        ("r-matrixstats" ,r-matrixstats)
@@ -11145,7 +11158,7 @@ droplet sequencing.  It has been particularly tailored for Drop-seq.")
 (define-public sambamba
   (package
     (name "sambamba")
-    (version "0.6.7-10-g223fa20")
+    (version "0.6.8")
     (source
      (origin
        (method git-fetch)
@@ -11155,7 +11168,7 @@ droplet sequencing.  It has been particularly tailored for Drop-seq.")
        (file-name (string-append name "-" version "-checkout"))
        (sha256
         (base32
-         "1zb9hrxglxqh13ava9wwri30cvf85hjnbn8ccnr8l60a3k5avczn"))))
+         "0k0cz3qcv98p6cq09zlbgnjsggxcqbcmzxg5zikgcgbr2nfq4lry"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; there is no test target
@@ -11166,9 +11179,10 @@ droplet sequencing.  It has been particularly tailored for Drop-seq.")
          (add-after 'unpack 'fix-ldc-version
            (lambda _
              (substitute* "gen_ldc_version_info.py"
-               (("/usr/bin/env.*") (which "python")))
+               (("/usr/bin/env.*") (which "python3")))
              (substitute* "Makefile"
-               (("\\$\\(shell which ldmd2\\)") (which "ldmd2")))
+               ;; We use ldc2 instead of ldmd2 to compile sambamba.
+               (("\\$\\(shell which ldmd2\\)") (which "ldc2")))
              #t))
          (add-after 'unpack 'place-biod-and-undead
            (lambda* (#:key inputs #:allow-other-keys)
@@ -11180,21 +11194,21 @@ droplet sequencing.  It has been particularly tailored for Drop-seq.")
              (substitute* "Makefile"
                (("htslib/libhts.a lz4/lib/liblz4.a")
                 "-L-lhts -L-llz4")
-               ((" htslib-static lz4-static") ""))
+               ((" lz4-static htslib-static") ""))
              #t))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out   (assoc-ref outputs "out"))
                     (bin   (string-append out "/bin")))
                (mkdir-p bin)
-               (install-file "build/sambamba" bin)
+               (install-file "bin/sambamba" bin)
                #t))))))
     (native-inputs
      `(("ldc" ,ldc)
        ("rdmd" ,rdmd)
-       ("python" ,python2-minimal)
+       ("python" ,python-minimal)
        ("biod"
-        ,(let ((commit "c778e4f2d8bacea7499283ce39f5577b232732c6"))
+        ,(let ((commit "4f1a7d2fb7ef3dfe962aa357d672f354ebfbe42e"))
            (origin
              (method git-fetch)
              (uri (git-reference
@@ -11205,20 +11219,20 @@ droplet sequencing.  It has been particularly tailored for Drop-seq.")
                                        "-checkout"))
              (sha256
               (base32
-               "1z90562hg47i63gx042wb3ak2vqjg5z7hwgn9bp2pdxfg3nxrw37")))))
+               "1k5pdjv1qvi0a3rwd1sfq6zbj37l86i7bf710m4c0y6737lxj426")))))
        ("undead"
-        ,(let ((commit "92803d25c88657e945511f0976a0c79d8da46e89"))
+        ,(let ((commit "9be93876982b5f14fcca60832563b3cd767dd84d"))
            (origin
              (method git-fetch)
              (uri (git-reference
-                   (url "https://github.com/dlang/undeaD.git")
+                   (url "https://github.com/biod/undeaD.git")
                    (commit commit)))
              (file-name (string-append "undead-"
                                        (string-take commit 9)
                                        "-checkout"))
              (sha256
               (base32
-               "0vq6n81vzqvgphjw54lz2isc1j8lcxwjdbrhqz1h5gwrvw9w5138")))))))
+               "1xfarj0nqlmi5jd1vmcmm7pabzaf9hxyvk6hp0d6jslb5k9r8r3d")))))))
     (inputs
      `(("lz4" ,lz4)
        ("htslib" ,htslib-for-sambamba)))
@@ -11234,16 +11248,16 @@ sort, markdup, and depth.")
 (define-public ritornello
   (package
     (name "ritornello")
-    (version "1.0.0")
+    (version "2.0.1")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/KlugerLab/"
-                                  "Ritornello/archive/v"
-                                  version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/KlugerLab/Ritornello.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "02nik86gq9ljjriv6pamwlmqnfky3ads1fpklx6mc3hx6k40pg38"))))
+                "1xahvq215qld7x1w8vpa5zbrsj6p9crb9shqa2x89sb0aaxa02jk"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; there are no tests
@@ -11252,7 +11266,7 @@ sort, markdup, and depth.")
          (add-after 'unpack 'patch-samtools-references
            (lambda* (#:key inputs #:allow-other-keys)
              (substitute* '("src/SamStream.h"
-                            "src/BufferedGenomeReader.h")
+                            "src/FLD.cpp")
                (("<sam.h>") "<samtools/sam.h>"))
              #t))
          (delete 'configure)
@@ -11478,15 +11492,16 @@ applications for tackling some common problems in a user-friendly way.")
 (define-public tadbit
   (package
     (name "tadbit")
-    (version "0.2")
+    (version "0.2.0")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/3DGenomes/TADbit/"
-                                  "archive/v" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/3DGenomes/TADbit.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1cnfqrl4685zar4nnw94j94nhvl2h29jm448nadqi1h05z6fdk4f"))))
+                "07g3aj648prmsvxp9caz5yl41k0y0647vxh0f5p3w8376mfiljd0"))))
     (build-system python-build-system)
     (arguments
      `(;; Tests are included and must be run after installation, but
@@ -11541,13 +11556,14 @@ models.  TADbit is complemented by TADkit for visualizing 3D models.")
     (version "302.0.0")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/ENCODE-DCC/kentUtils/"
-                           "archive/v" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/ENCODE-DCC/kentUtils.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "134aja3k1cj32kbk1nnw0q9gxjb2krr15q6sga8qldzvc0585rmm"))
+         "0n1wbyjpzii2b9qhyp9r1q76j623cggpg3y8fmw78ld3z4y7ivha"))
        (modules '((guix build utils)
                   (srfi srfi-26)
                   (ice-9 ftw)))
@@ -11598,6 +11614,8 @@ models.  TADbit is complemented by TADkit for visualizing 3D models.")
        #:tests? #f
        #:phases
        (modify-phases %standard-phases
+         (add-after 'unpack 'fix-permissions
+           (lambda _ (make-file-writable "src/inc/localEnvironment.mk") #t))
          (add-after 'unpack 'fix-paths
            (lambda _
              (substitute* "Makefile"
@@ -11893,14 +11911,14 @@ accurate as existing quantification tools.")
     (name "libgff")
     (version "1.0")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/Kingsford-Group/"
-                    "libgff/archive/v" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/Kingsford-Group/libgff.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0vc4nxyhlm6g9vvmx5l4lfs5pnvixsv1hiiy4kddf2y3p6jna8ls"))))
+                "0n6vfjnq7a2mianipscbshrvbncss8z4zkgkbjw754p9043nfkps"))))
     (build-system cmake-build-system)
     (arguments `(#:tests? #f))          ; no tests included
     (home-page "https://github.com/Kingsford-Group/libgff")
@@ -11945,14 +11963,14 @@ bytes of memory space, where n is the length of the string.")
     (name "sailfish")
     (version "0.10.1")
     (source (origin
-              (method url-fetch)
-              (uri
-               (string-append "https://github.com/kingsfordgroup/"
-                              "sailfish/archive/v" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/kingsfordgroup/sailfish.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1inn60dxiwsz8g9w7kvfhjxj4bwfb0r12dyhpzzhfbig712dkmm0"))
+                "1amcc5hqvsl42hg4x19bi9vy47cl874s0lw1fmi0hwsdk9i8c03v"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -12000,10 +12018,10 @@ bytes of memory space, where n is the length of the string.")
                    (include "external/install/include/rapmap/")
                    (rapmap (assoc-ref inputs "rapmap")))
                (mkdir-p "/tmp/rapmap")
-               (system* "tar" "xf"
-                        (assoc-ref inputs "rapmap")
-                        "-C" "/tmp/rapmap"
-                        "--strip-components=1")
+               (invoke "tar" "xf"
+                       (assoc-ref inputs "rapmap")
+                       "-C" "/tmp/rapmap"
+                       "--strip-components=1")
                (mkdir-p src)
                (mkdir-p include)
                (for-each (lambda (file)
@@ -14101,6 +14119,85 @@ enrichment analysis (GSEA) calculation with or without the absolute filtering.
 absolute GSEA.")
     (license license:gpl2)))
 
+(define-public jamm
+  (package
+    (name "jamm")
+    (version "1.0.7.5")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/mahmoudibrahim/JAMM.git")
+             (commit (string-append "JAMMv" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0ls889jcma1ch9h21jjhnkadgszgqj41842hhcjh6cg88f85qf3i"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; there are none
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (replace 'build
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (substitute* "JAMM.sh"
+               (("^sPath=.*")
+                (string-append "")))
+             #t))
+         (replace 'install
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (libexec (string-append out "/libexec/jamm"))
+                    (bin (string-append out "/bin")))
+               (substitute* '("JAMM.sh"
+                              "SignalGenerator.sh")
+                 (("^sPath=.*")
+                  (string-append "sPath=\"" libexec "\"\n")))
+               (for-each (lambda (file)
+                           (install-file file libexec))
+                         (list "bincalculator.r"
+                               "peakfinder.r"
+                               "peakhelper.r"
+                               "signalmaker.r"
+                               "xcorr.r"
+                               "xcorrhelper.r"
+                               ;; Perl scripts
+                               "peakfilter.pl"
+                               "readshifter.pl"))
+
+               (for-each
+                (lambda (script)
+                  (chmod script #o555)
+                  (install-file script bin)
+                  (wrap-program (string-append bin "/" script)
+                    `("PATH" ":" prefix
+                      (,(string-append (assoc-ref inputs "coreutils") "/bin")
+                       ,(string-append (assoc-ref inputs "gawk") "/bin")
+                       ,(string-append (assoc-ref inputs "perl") "/bin")
+                       ,(string-append (assoc-ref inputs "r-minimal") "/bin")))
+                    `("PERL5LIB" ":" prefix (,(getenv "PERL5LIB")))
+                    `("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE")))))
+                (list "JAMM.sh" "SignalGenerator.sh")))
+             #t)))))
+    (inputs
+     `(("bash" ,bash)
+       ("coreutils" ,coreutils)
+       ("gawk" ,gawk)
+       ("perl" ,perl)
+       ("r-minimal" ,r-minimal)
+       ;;("r-parallel" ,r-parallel)
+       ("r-signal" ,r-signal)
+       ("r-mclust" ,r-mclust)))
+    (home-page "https://github.com/mahmoudibrahim/JAMM")
+    (synopsis "Peak finder for NGS datasets")
+    (description
+     "JAMM is a peak finder for next generation sequencing datasets (ChIP-Seq,
+ATAC-Seq, DNase-Seq, etc.) that can integrate replicates and assign peak
+boundaries accurately.  JAMM is applicable to both broad and narrow
+datasets.")
+    (license license:gpl3+)))
+
 (define-public ngless
   (package
     (name "ngless")
@@ -14123,9 +14220,30 @@ absolute GSEA.")
        #:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'create-cabal-file
-           (lambda _ (invoke "hpack") #t)))))
+           (lambda _ (invoke "hpack") #t))
+         ;; These tools are expected to be installed alongside ngless.
+         (add-after 'install 'link-tools
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
+               (symlink (string-append (assoc-ref inputs "prodigal")
+                                       "/bin/prodigal")
+                        (string-append bin "ngless-" ,version "-prodigal"))
+               (symlink (string-append (assoc-ref inputs "minimap2")
+                                       "/bin/minimap2")
+                        (string-append bin "ngless-" ,version "-minimap2"))
+               (symlink (string-append (assoc-ref inputs "samtools")
+                                       "/bin/samtools")
+                        (string-append bin "ngless-" ,version "-samtools"))
+               (symlink (string-append (assoc-ref inputs "bwa")
+                                       "/bin/bwa")
+                        (string-append bin "ngless-" ,version "-bwa"))
+               #t))))))
     (inputs
-     `(("ghc-aeson" ,ghc-aeson)
+     `(("prodigal" ,prodigal)
+       ("bwa" ,bwa)
+       ("samtools" ,samtools)
+       ("minimap2" ,minimap2)
+       ("ghc-aeson" ,ghc-aeson)
        ("ghc-ansi-terminal" ,ghc-ansi-terminal)
        ("ghc-async" ,ghc-async)
        ("ghc-atomic-write" ,ghc-atomic-write)
@@ -14244,3 +14362,77 @@ both read length (longer is better) and read identity (higher is better) when
 choosing which reads pass the filter.")
       (license (list license:gpl3       ;filtlong
                      license:asl2.0))))) ;histogram.py
+
+(define-public nanopolish
+  ;; The recommended way to install is to clone the git repository
+  ;; <https://github.com/jts/nanopolish#installing-a-particular-release>.
+  ;; Also, the differences between release and current version seem to be
+  ;; significant.
+  (let ((commit "50e8b5cc62f9b46f5445f5c5e8c5ab7263ea6d9d")
+        (revision "1"))
+    (package
+      (name "nanopolish")
+      (version (git-version "0.10.2" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/jts/nanopolish.git")
+               (commit commit)
+               (recursive? #t)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "09j5gz57yr9i34a27vbl72i4g8syv2zzgmsfyjq02yshmnrvkjs6"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:make-flags
+         `("HDF5=noinstall" "EIGEN=noinstall" "HTS=noinstall" "CC=gcc")
+         #:tests? #f                    ; no check target
+         #:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'find-eigen
+             (lambda* (#:key inputs #:allow-other-keys)
+               (setenv "CPATH"
+                       (string-append (assoc-ref inputs "eigen")
+                                      "/include/eigen3"))
+               #t))
+           (delete 'configure)
+           (replace 'install
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let* ((out (assoc-ref outputs "out"))
+                      (bin (string-append out "/bin"))
+                      (scripts (string-append out "/share/nanopolish/scripts")))
+
+                 (install-file "nanopolish" bin)
+                 (for-each (lambda (file) (install-file file scripts))
+                           (find-files "scripts" ".*"))
+                 #t)))
+           (add-after 'install 'wrap-programs
+             (lambda* (#:key outputs #:allow-other-keys)
+               (for-each (lambda (file)
+                           (wrap-program file `("PYTHONPATH" ":" prefix (,path))))
+                         (find-files "/share/nanopolish/scripts" "\\.py"))
+               (for-each (lambda (file)
+                           (wrap-program file `("PERL5LIB" ":" prefix (,path))))
+                         (find-files  "/share/nanopolish/scripts" "\\.pl"))
+               #t)))))
+      (inputs
+       `(("eigen" ,eigen)
+         ("hdf5" ,hdf5)
+         ("htslib" ,htslib)
+         ("perl" ,perl)
+         ("python" ,python)
+         ("python-biopython" ,python-biopython)
+         ("python-numpy" ,python-numpy)
+         ("python-pysam" ,python-pysam)
+         ("python-scikit-learn" , python-scikit-learn)
+         ("python-scipy" ,python-scipy)
+         ("zlib" ,zlib)))
+      (home-page "https://github.com/jts/nanopolish")
+      (synopsis "Signal-level analysis of Oxford Nanopore sequencing data")
+      (description
+       "This package analyses the Oxford Nanopore sequencing data at signal-level.
+Nanopolish can calculate an improved consensus sequence for a draft genome
+assembly, detect base modifications, call SNPs (Single nucleotide
+polymorphisms) and indels with respect to a reference genome and more.")
+      (license license:expat))))
jackhill's copy of GNU Guix: https://guix.gnu.org/