From 948a94d13b6ce9e89a03d1ba76ae613cba26dc01 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 15 Jan 2025 13:02:10 +0100
Subject: gnu: Add fast5.

Moved here from guix-science.

* gnu/packages/bioinformatics.scm (fast5): New variable.

Change-Id: I3373be5d5c80f3600b88fd3f71eadf723443e1c9
---
 gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

(limited to 'gnu')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1bf0b4b09a..7a3eebf23d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7433,6 +7433,45 @@ variety of diversity measures including those that make use of phylogenetic
 similarity of community members.")
    (license license:gpl3+)))
 
+(define-public fast5
+  (package
+    (name "fast5")
+    (version "0.6.5")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/mateidavid/fast5")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1dsq3x1662ck1bcmcmqhblnhmypfppgysblgj2xr4lr6fl4si4pk"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:tests? #f                       ;There are no tests.
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'use-system-hdf5
+            (lambda* (#:key inputs outputs #:allow-other-keys)
+              (setenv "HDF5_INCLUDE_DIR"
+                      (string-append #$(this-package-input "hdf5") "/include"))
+              (setenv "HDF5_LIB_DIR"
+                      (string-append #$(this-package-input "hdf5") "/lib"))))
+          (add-after 'unpack 'chdir
+            (lambda _
+              (chdir "python"))))))
+    (inputs (list hdf5))
+    (propagated-inputs
+     (list python-dateutil))
+    (native-inputs
+     (list python-cython python-setuptools python-wheel))
+    (home-page "https://github.com/mateidavid/fast5")
+    (synopsis "Library for accessing Oxford Nanopore sequencing data")
+    (description "This package provides a lightweight C++ library for accessing
+Oxford Nanopore Technologies sequencing data.")
+    (license license:expat)))
+
 (define-public fanc
   (let ((commit "354401e52ba2320e6b1ba0d3b5aab3541d31c9f3")
 	(revision "1"))
-- 
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