From d9b40f6397de11c3d59001fa9a5cec226ee408c1 Mon Sep 17 00:00:00 2001
From: scalavision <scalavision@gmail.com>
Date: Thu, 31 Oct 2019 19:34:05 +0100
Subject: [PATCH] deeptools: init at 3.3.1

---
 .../science/biology/deeptools/default.nix     | 42 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  2 +
 2 files changed, 44 insertions(+)
 create mode 100644 pkgs/applications/science/biology/deeptools/default.nix

diff --git a/pkgs/applications/science/biology/deeptools/default.nix b/pkgs/applications/science/biology/deeptools/default.nix
new file mode 100644
index 000000000000..78a6f483337f
--- /dev/null
+++ b/pkgs/applications/science/biology/deeptools/default.nix
@@ -0,0 +1,42 @@
+{ lib
+, python
+}:
+with python.pkgs;
+buildPythonApplication rec {
+  pname = "deepTools";
+  version = "3.3.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "08p36p9ncj5s8qf1r7h83x4rnmi63l3yk6mnr3wgpg2qgvwl0hji";
+  };
+
+  propagatedBuildInputs = [
+    numpy
+    numpydoc
+    scipy
+    py2bit
+    pybigwig
+    pysam
+    matplotlib
+    plotly
+    deeptoolsintervals
+  ];
+
+  checkInputs = [ pytest ];
+
+  meta = with lib; {
+    homepage = "https://deeptools.readthedocs.io/en/develop";
+    description = "Tools for exploring deep DNA sequencing data";
+    longDescription = ''
+      deepTools contains useful modules to process the mapped reads data for multiple
+      quality checks, creating normalized coverage files in standard bedGraph and bigWig
+      file formats, that allow comparison between different files (for example, treatment and control).
+      Finally, using such normalized and standardized files, deepTools can create many
+      publication-ready visualizations to identify enrichments and for functional
+      annotations of the genome.
+    '';
+    license = licenses.gpl3;
+    maintainers = with maintainers; [ scalavision ];
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 1be6d168b03c..6e8fe9ac305a 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -23286,6 +23286,8 @@ in
 
   dcm2niix = callPackage ../applications/science/biology/dcm2niix { };
 
+  deeptools = callPackage ../applications/science/biology/deeptools { python = python3; };
+
   delly = callPackage ../applications/science/biology/delly { };
 
   diamond = callPackage ../applications/science/biology/diamond { };