From 81bfbe3d828a3e0a71a10562c4ec6516cdd5607d Mon Sep 17 00:00:00 2001
From: Alexis Praga <alexis@praga.dev>
Date: Mon, 18 Nov 2024 00:04:31 +0100
Subject: [PATCH 1/3] ropebwt2: init at 0-unstable-2021-02-01

Tiddit dependency. GCC use is hardcoded in Makefile so CC is overridden
to use clang on other platforms.
---
 pkgs/by-name/ro/ropebwt2/package.nix | 31 ++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 pkgs/by-name/ro/ropebwt2/package.nix

diff --git a/pkgs/by-name/ro/ropebwt2/package.nix b/pkgs/by-name/ro/ropebwt2/package.nix
new file mode 100644
index 000000000000..c83512b71912
--- /dev/null
+++ b/pkgs/by-name/ro/ropebwt2/package.nix
@@ -0,0 +1,31 @@
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  zlib,
+}:
+stdenv.mkDerivation {
+  name = "ropebwt2";
+  version = "0-unstable-2021-02-01";
+  src = fetchFromGitHub {
+    owner = "lh3";
+    repo = "ropebwt2";
+    rev = "bd8dbd3db2e9e3cff74acc2907c0742c9ebbf033";
+    hash = "sha256-R/VvbprwcfXF2TBZOYmc1MU3AzCcXFfWCHoYYumXtI8=";
+  };
+  buildInputs = [ zlib ];
+  makeFlags = [ "CC=${stdenv.cc.targetPrefix}cc" ];
+  installPhase = ''
+    runHook preInstall
+    install -Dm755 ropebwt2 -t $out/bin
+    runHook postInstall
+  '';
+  meta = {
+    homepage = "https://github.com/lh3/ropebwt2";
+    description = "Incremental construction of FM-index for DNA sequences";
+    mainProgram = "ropebwwith lib; t2";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ apraga ];
+    platforms = lib.platforms.unix;
+  };
+}

From 602605237b42660be3b3deab3fef3a0576140a7a Mon Sep 17 00:00:00 2001
From: Alexis Praga <alexis@praga.dev>
Date: Mon, 18 Nov 2024 00:07:28 +0100
Subject: [PATCH 2/3] fermi2: init at unstable-2021-05-21

Tiddit dependency.
---
 pkgs/by-name/fe/fermi2/package.nix | 34 ++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 pkgs/by-name/fe/fermi2/package.nix

diff --git a/pkgs/by-name/fe/fermi2/package.nix b/pkgs/by-name/fe/fermi2/package.nix
new file mode 100644
index 000000000000..9d391b476edc
--- /dev/null
+++ b/pkgs/by-name/fe/fermi2/package.nix
@@ -0,0 +1,34 @@
+{
+  config,
+  lib,
+  fetchFromGitHub,
+  zlib,
+  stdenv,
+}:
+stdenv.mkDerivation {
+  pname = "fermi2";
+  version = "0.1-unstable-2021-05-21";
+  src = fetchFromGitHub {
+    owner = "lh3";
+    repo = "fermi2";
+    rev = "cb1410972b2bd330883823116931ae67ead8b30f";
+    hash = "sha256-jDn1OBuGWDMEHI5A3R9meOykEGM6yjItSnUpx36DxgA=";
+  };
+  buildInputs = [ zlib ];
+  makeFlags = [ "CC=${stdenv.cc.targetPrefix}cc" ];
+  installPhase = ''
+    runHook preInstall
+
+    install -Dm755 fermi2 -t $out/bin
+
+    runHook postInstall
+  '';
+  meta = {
+    homepage = "https://github.com/lh3/fermi2";
+    description = "Successor of fermi, a whole genome de novo assembler based on the FMD-index for large genomes";
+    mainProgram = "fermi2";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ apraga ];
+    platforms = lib.intersectLists lib.platforms.x86_64 lib.platforms.unix;
+  };
+}

From 196f141973be2bed412b7e8cc016afb65c2d7254 Mon Sep 17 00:00:00 2001
From: Alexis Praga <alexis@praga.dev>
Date: Sun, 17 Nov 2024 23:02:20 +0100
Subject: [PATCH 3/3] tiddit: init at 3.6.1

Genomic tool to call structural variations.

This packages requires 2 executables,packaging fermi2, bwt2, that are
packaged in the same derivation and added to the path later on.
---
 pkgs/by-name/ro/ropebwt2/package.nix |  4 ++-
 pkgs/by-name/ti/tiddit/package.nix   | 51 ++++++++++++++++++++++++++++
 2 files changed, 54 insertions(+), 1 deletion(-)
 create mode 100644 pkgs/by-name/ti/tiddit/package.nix

diff --git a/pkgs/by-name/ro/ropebwt2/package.nix b/pkgs/by-name/ro/ropebwt2/package.nix
index c83512b71912..3ef831907e7d 100644
--- a/pkgs/by-name/ro/ropebwt2/package.nix
+++ b/pkgs/by-name/ro/ropebwt2/package.nix
@@ -17,13 +17,15 @@ stdenv.mkDerivation {
   makeFlags = [ "CC=${stdenv.cc.targetPrefix}cc" ];
   installPhase = ''
     runHook preInstall
+
     install -Dm755 ropebwt2 -t $out/bin
+
     runHook postInstall
   '';
   meta = {
     homepage = "https://github.com/lh3/ropebwt2";
     description = "Incremental construction of FM-index for DNA sequences";
-    mainProgram = "ropebwwith lib; t2";
+    mainProgram = "ropebwt2";
     license = lib.licenses.mit;
     maintainers = with lib.maintainers; [ apraga ];
     platforms = lib.platforms.unix;
diff --git a/pkgs/by-name/ti/tiddit/package.nix b/pkgs/by-name/ti/tiddit/package.nix
new file mode 100644
index 000000000000..4ec1b496360e
--- /dev/null
+++ b/pkgs/by-name/ti/tiddit/package.nix
@@ -0,0 +1,51 @@
+{
+  bwa,
+  lib,
+  fermi2,
+  ropebwt2,
+  fetchFromGitHub,
+  python3Packages,
+}:
+python3Packages.buildPythonApplication rec {
+  name = "tiddit";
+  version = "3.6.1";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "SciLifeLab";
+    repo = "TIDDIT";
+    rev = "refs/tags/TIDDIT-${version}";
+    hash = "sha256-OeqVQJDw0fmSDWIGab2qtTJCzZxqLY2XzRqaTRuPIdI=";
+  };
+
+  build-system = with python3Packages; [
+    setuptools
+    wheel
+  ];
+
+  dependencies = with python3Packages; [
+    cython
+    joblib
+    numpy
+    pysam
+  ];
+
+  makeWrapperArgs = [
+    "--prefix PATH : ${
+      lib.makeBinPath [
+        bwa
+        fermi2
+        ropebwt2
+      ]
+    }"
+  ];
+
+  meta = {
+    homepage = "https://github.com/SciLifeLab/TIDDIT";
+    description = "Identify chromosomal rearrangements using Mate Pair or Paired End sequencing data";
+    mainProgram = "tiddit";
+    license = lib.licenses.gpl3Only;
+    maintainers = with lib.maintainers; [ apraga ];
+    platforms = lib.platforms.unix;
+  };
+}