From 7f55904558e0f481d2f60ab52510c7e126c73fd0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 26 Apr 2019 14:57:29 +0200
Subject: [PATCH] gnu: Add umi-tools.

* gnu/packages/bioinformatics.scm (umi-tools): New variable.
---
 gnu/packages/bioinformatics.scm | 35 +++++++++++++++++++++++++++++++++
 gnu/packages/music.scm          |  2 ++
 2 files changed, 37 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4cf6900498..4891bb15af 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14739,3 +14739,38 @@ tools for identifying genome bins that are likely candidates for merging based
 on marker set compatibility, similarity in genomic characteristics, and
 proximity within a reference genome.")
     (license license:gpl3+)))
+
+(define-public umi-tools
+  (package
+    (name "umi-tools")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "umi_tools" version))
+       (sha256
+        (base32
+         "08y3vz1vcx09whmbsn722lcs6jl9wyrh9i4p3k8j4cb1i32bij4a"))))
+    (build-system python-build-system)
+    (inputs
+     `(("python-setuptools" ,python-setuptools)
+       ("python-pandas" ,python-pandas)
+       ("python-future" ,python-future)
+       ("python-scipy" ,python-scipy)
+       ("python-matplotlib" ,python-matplotlib)
+       ("python-regex" ,python-regex)
+       ("python-pysam" ,python-pysam)))
+    (native-inputs
+     `(("python-setuptools" ,python-setuptools)
+       ("python-cython" ,python-cython)))
+    (home-page "https://github.com/CGATOxford/UMI-tools")
+    (synopsis "Tools for analyzing unique modular identifiers")
+    (description "This package provides tools for dealing with @dfn{Unique
+Molecular Identifiers} (UMIs) and @dfn{Random Molecular Tags} (RMTs) in
+genetic sequences.  There are six tools: the @code{extract} and
+@code{whitelist} commands are used to prepare a fastq containg UMIs @code{+/-}
+cell barcodes for alignment.  The remaining commands, @code{group},
+@code{dedup}, and @{count}/@code{count_tab}, are used to identify PCR
+duplicates using the UMIs and perform different levels of analysis depending
+on the needs of the user.")
+    (license license:expat)))
diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 29b448fc9a..aafe420d04 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -54,6 +54,7 @@
   #:use-module (guix build-system trivial)
   #:use-module (guix build-system go)
   #:use-module (gnu packages)
+  #:use-module (gnu packages admin)
   #:use-module (gnu packages algebra)
   #:use-module (gnu packages apr)
   #:use-module (gnu packages audio)
@@ -94,6 +95,7 @@
   #:use-module (gnu packages gstreamer)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages guile)
+  #:use-module (gnu packages haskell)
   #:use-module (gnu packages image)
   #:use-module (gnu packages imagemagick)
   #:use-module (gnu packages java)