gnu: nanopolish: Update to 0.14.0.

* gnu/packages/bioinformatics.scm (nanopolish): Update to 0.14.0.
[source]: Update snippet.
[arguments]: Use gexp; use cc-for-target; drop #T from build phases.
[inputs]: Add minimap2.
[native-inputs]: Add cmake-minimal.

gnu/packages/bioinformatics.scm

@@ -14358,37 +14358,36 @@ choosing which reads pass the filter.")
                      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 "6331dc4f15b9dfabb954ba3fae9d76b6c3ca6377")
-        (revision "1"))
   (package
     (name "nanopolish")
-      (version (git-version "0.11.1" revision commit))
+    (version "0.14.0")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/jts/nanopolish")
-               (commit commit)
+             (commit (string-append "v" version))
              (recursive? #t)))
        (file-name (git-file-name name version))
        (sha256
-          (base32 "15ikl3d37y49pwd7vx36xksgsqajhf24q7qqsnpl15dqqyy5qgbc"))
+        (base32 "1ha9v5ia0qrwgav0956cfc7n64wjm9a9w3rvkg21g37a994yixg5"))
        (modules '((guix build utils)))
        (snippet
-          '(begin
-             (delete-file-recursively "htslib")
-             #t))))
+        ;; TODO: unbundle slow5lib
+        '(begin (for-each delete-file-recursively
+                          '("htslib" "minimap2"))))))
     (build-system gnu-build-system)
     (arguments
-       `(#:make-flags
-         `("HDF5=noinstall" "EIGEN=noinstall" "HTS=noinstall" "CC=gcc")
+     (list
+      #:make-flags
+      #~(list "HDF5=noinstall"
+              "EIGEN=noinstall"
+              "HTS=noinstall"
+              "MINIMAP2=noinstall"
+              (string-append "CC=" #$(cc-for-target)))
       #:tests? #f                    ; no check target
       #:phases
-         (modify-phases %standard-phases
+      #~(modify-phases %standard-phases
           (add-after 'unpack 'find-eigen
             (lambda* (#:key inputs #:allow-other-keys)
               (setenv "CPATH"
@@ -14397,21 +14396,18 @@ choosing which reads pass the filter.")
                        ":" (or (getenv "CPATH") "")))))
           (delete 'configure)
           (replace 'install
-             (lambda* (#:key outputs #:allow-other-keys)
-               (let* ((out (assoc-ref outputs "out"))
-                      (bin (string-append out "/bin"))
-                      (scripts (string-append out "/share/nanopolish/scripts")))
+            (lambda _
+              (let ((bin (string-append #$output "/bin"))
+                    (scripts (string-append #$output "/share/nanopolish/scripts")))
 
                 (install-file "nanopolish" bin)
                 (for-each (lambda (file) (install-file file scripts))
-                           (find-files "scripts" ".*"))
-                 #t)))
+                          (find-files "scripts" ".*")))))
           (add-after 'install 'wrap-programs
-             (lambda* (#:key inputs outputs #:allow-other-keys)
+            (lambda* (#:key inputs #:allow-other-keys)
               (let ((pythonpath (getenv "GUIX_PYTHONPATH"))
                     (perl5lib (getenv "PERL5LIB"))
-                     (scripts (string-append (assoc-ref outputs "out")
-                                             "/share/nanopolish/scripts"))
+                    (scripts (string-append #$output "/share/nanopolish/scripts"))
                     (guile (search-input-file inputs "bin/guile")))
                 (for-each (lambda (file)
                             (wrap-program file `("GUIX_PYTHONPATH" ":" prefix (,pythonpath))))
@@ -14425,6 +14421,7 @@ choosing which reads pass the filter.")
        ("eigen" ,eigen)
        ("hdf5" ,hdf5)
        ("htslib" ,htslib)
+       ("minimap2" ,minimap2)
        ("perl" ,perl)
        ("bioperl" ,bioperl-minimal)
        ("perl-getopt-long" ,perl-getopt-long)
@@ -14435,6 +14432,7 @@ choosing which reads pass the filter.")
        ("python-scikit-learn" , python-scikit-learn)
        ("python-scipy" ,python-scipy)
        ("zlib" ,zlib)))
+    (native-inputs (list cmake-minimal))
     (home-page "https://github.com/jts/nanopolish")
     (synopsis "Signal-level analysis of Oxford Nanopore sequencing data")
     (description
@@ -14442,7 +14440,7 @@ choosing which reads pass the filter.")
 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))))
+    (license license:expat)))
 
 (define-public cnvkit
   (package