From 19e42618376e92cb9745197642ff5cb4afa39945 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 14 Oct 2019 22:37:54 +0200
Subject: gnu: Add methyldackel.

* gnu/packages/bioinformatics.scm (methyldackel): New variable.
---
 gnu/packages/bioinformatics.scm | 44 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 12c30236cb..5f57a59b06 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -15304,3 +15304,47 @@ (define-public r-velocyto
 transcriptional derivatives and visualization of the resulting velocity
 patterns.")
       (license license:gpl3))))
+
+(define-public methyldackel
+  (package
+    (name "methyldackel")
+    (version "0.4.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/dpryan79/MethylDackel.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "10gh8k0ca92kywnrw5pkacq3g6r8s976s12k8jhp8g3g49q9a97g"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:test-target "test"
+       #:make-flags
+       (list "CC=gcc"
+             (string-append "prefix="
+                            (assoc-ref %outputs "out") "/bin/"))
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'configure
+           (lambda* (#:key outputs #:allow-other-keys)
+             (substitute* "Makefile"
+               (("install MethylDackel \\$\\(prefix\\)" match)
+                (string-append "install -d $(prefix); " match)))
+             #t)))))
+    (inputs
+     `(("htslib" ,htslib)
+       ("zlib" ,zlib)))
+    ;; Needed for tests
+    (native-inputs
+     `(("python" ,python-wrapper)))
+    (home-page "https://github.com/dpryan79/MethylDackel")
+    (synopsis "Universal methylation extractor for BS-seq experiments")
+    (description
+     "MethylDackel will process a coordinate-sorted and indexed BAM or CRAM
+file containing some form of BS-seq alignments and extract per-base
+methylation metrics from them.  MethylDackel requires an indexed fasta file
+containing the reference genome as well.")
+    ;; See https://github.com/dpryan79/MethylDackel/issues/85
+    (license license:expat)))
-- 
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