From 72974392fc7edb85362be9eaab3e8247d8ebe9dd Mon Sep 17 00:00:00 2001
From: Pavol Rusnak <pavol@rusnak.io>
Date: Fri, 1 Jan 2021 19:22:17 +0100
Subject: [PATCH 1/3] python3Packages.flametree: init at 0.1.11

---
 .../python-modules/flametree/default.nix      | 26 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  2 ++
 2 files changed, 28 insertions(+)
 create mode 100644 pkgs/development/python-modules/flametree/default.nix

diff --git a/pkgs/development/python-modules/flametree/default.nix b/pkgs/development/python-modules/flametree/default.nix
new file mode 100644
index 00000000000..d4cba69afcb
--- /dev/null
+++ b/pkgs/development/python-modules/flametree/default.nix
@@ -0,0 +1,26 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+}:
+
+buildPythonPackage rec {
+  pname = "flametree";
+  version = "0.1.11";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "c8eb81dea8c7f8261a2aa03d2bac98b1d21ebceec9c67efaac423f7c1b4fe061";
+  };
+
+  # no tests in tarball
+  doCheck = false;
+
+  pythonImportsCheck = [ "flametree" ];
+
+  meta = with lib; {
+    homepage = "https://github.com/Edinburgh-Genome-Foundry/Flametree";
+    description = "Python file and zip operations made easy";
+    license = licenses.mit;
+    maintainers = with maintainers; [ prusnak ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 57458230bb1..4ca83318c8a 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -2139,6 +2139,8 @@ in {
 
   flaky = callPackage ../development/python-modules/flaky { };
 
+  flametree = callPackage ../development/python-modules/flametree { };
+
   flammkuchen = callPackage ../development/python-modules/flammkuchen { };
 
   flask-admin = callPackage ../development/python-modules/flask-admin { };

From aa30970bc95c4f270cff1769af582919b7a80687 Mon Sep 17 00:00:00 2001
From: Pavol Rusnak <pavol@rusnak.io>
Date: Fri, 1 Jan 2021 19:28:29 +0100
Subject: [PATCH 2/3] python3Packages.python-codon-tables: init at 0.1.10

---
 .../python-codon-tables/default.nix           | 27 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  2 ++
 2 files changed, 29 insertions(+)
 create mode 100644 pkgs/development/python-modules/python-codon-tables/default.nix

diff --git a/pkgs/development/python-modules/python-codon-tables/default.nix b/pkgs/development/python-modules/python-codon-tables/default.nix
new file mode 100644
index 00000000000..4c1ec6a3a20
--- /dev/null
+++ b/pkgs/development/python-modules/python-codon-tables/default.nix
@@ -0,0 +1,27 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+}:
+
+buildPythonPackage rec {
+  pname = "python-codon-tables";
+  version = "0.1.10";
+
+  src = fetchPypi {
+    pname = "python_codon_tables";
+    inherit version;
+    sha256 = "265beac928cbb77c6745bc728471adc7ffef933b794be303d272ecb9ad37d3d4";
+  };
+
+  # no tests in tarball
+  doCheck = false;
+
+  pythonImportsCheck = [ "python_codon_tables" ];
+
+  meta = with lib; {
+    homepage = "https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables";
+    description = "Codon Usage Tables for Python, from kazusa.or.jp";
+    license = licenses.mit;
+    maintainers = with maintainers; [ prusnak ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 4ca83318c8a..af921af1cd9 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -4687,6 +4687,8 @@ in {
 
   pysbd = callPackage ../development/python-modules/pysbd { };
 
+  python-codon-tables = callPackage ../development/python-modules/python-codon-tables { };
+
   python-csxcad = callPackage ../development/python-modules/python-csxcad { };
 
   python-openems = callPackage ../development/python-modules/python-openems { };

From c6db0dab11537f21ce55cb507760eb67d83e9c9d Mon Sep 17 00:00:00 2001
From: Pavol Rusnak <pavol@rusnak.io>
Date: Fri, 1 Jan 2021 19:34:29 +0100
Subject: [PATCH 3/3] python3Packages.dnachisel: init at 3.2.5

---
 .../python-modules/dnachisel/default.nix      | 41 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  2 +
 2 files changed, 43 insertions(+)
 create mode 100644 pkgs/development/python-modules/dnachisel/default.nix

diff --git a/pkgs/development/python-modules/dnachisel/default.nix b/pkgs/development/python-modules/dnachisel/default.nix
new file mode 100644
index 00000000000..465f1bb5b4d
--- /dev/null
+++ b/pkgs/development/python-modules/dnachisel/default.nix
@@ -0,0 +1,41 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, biopython
+, docopt
+, flametree
+, numpy
+, proglog
+, python-codon-tables
+ }:
+
+buildPythonPackage rec {
+  pname = "dnachisel";
+  version = "3.2.5";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "35301c5eda0baca5902403504e0b5a22eb65da92c2bbd23199d95c4a6bf0ef37";
+  };
+
+  propagatedBuildInputs = [
+    biopython
+    docopt
+    flametree
+    numpy
+    proglog
+    python-codon-tables
+  ];
+
+  # no tests in tarball
+  doCheck = false;
+
+  pythonImportsCheck = [ "dnachisel" ];
+
+  meta = with lib; {
+    homepage = "https://github.com/Edinburgh-Genome-Foundry/DnaChisel";
+    description = "Optimize DNA sequences under constraints";
+    license = licenses.mit;
+    maintainers = with maintainers; [ prusnak ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index af921af1cd9..05abf503128 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -1793,6 +1793,8 @@ in {
 
   dm-sonnet = callPackage ../development/python-modules/dm-sonnet { };
 
+  dnachisel = callPackage ../development/python-modules/dnachisel { };
+
   dnslib = callPackage ../development/python-modules/dnslib { };
 
   dnspython = if isPy3k then