gnu: Add mosaicatcher.

* gnu/packages/bioinformatics.scm (mosaicatcher): New variable.

gnu/packages/bioinformatics.scm

@@ -6170,6 +6170,46 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
       ;; 2. MD5 implementation - RSA Data Security, RFC 1321
       (license (list license:gpl2+ license:public-domain)))))
 
+(define-public mosaicatcher
+  (package
+    (name "mosaicatcher")
+    (version "0.3.1")
+    (source (origin
+              ;; There are no release tarballs nor tags.
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/friendsofstrandseq/mosaicatcher")
+                    (commit (string-append version "-dev"))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1n2s5wvvj2y0vfgjkg1q11xahpbagxz7h2vf5q7qyy25s12kbzbd"))
+              (patches (search-patches "mosaicatcher-unbundle-htslib.patch"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:tests? #false ; there are no tests
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'chdir
+           (lambda _ (chdir "src")))
+         (replace 'install
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let* ((target (assoc-ref outputs "out"))
+                    (bin (string-append target "/bin"))
+                    (share (string-append target "/share/mosaicatcher")))
+               (install-file "mosaic" bin)
+               (mkdir-p share)
+               (copy-recursively "../R" share)))))))
+    (inputs
+     `(("boost" ,boost)
+       ("htslib" ,htslib)))
+    (home-page "https://github.com/friendsofstrandseq/mosaicatcher")
+    (synopsis "Count and classify Strand-seq reads")
+    (description
+     "Mosaicatcher counts Strand-seq reads and classifies strand states of
+each chromosome in each cell using a Hidden Markov Model.")
+    (license license:expat)))
+
 (define-public ngs-sdk
   (package
     (name "ngs-sdk")