From 2bd2c3958ed91ef3bbea2fc3e077a8c03a648a1b Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Mon, 16 May 2022 12:46:12 +1000
Subject: quip: init

---
 tools/quip-app.nix    | 19 +++++++++++++++++++
 tools/quip-quip.nix   | 17 +++++++++++++++++
 tools/quip-unquip.nix | 18 ++++++++++++++++++
 tools/quip.nix        |  6 ++++++
 4 files changed, 60 insertions(+)
 create mode 100644 tools/quip-app.nix
 create mode 100644 tools/quip-quip.nix
 create mode 100644 tools/quip-unquip.nix
 create mode 100644 tools/quip.nix

(limited to 'tools')

diff --git a/tools/quip-app.nix b/tools/quip-app.nix
new file mode 100644
index 0000000..422b603
--- /dev/null
+++ b/tools/quip-app.nix
@@ -0,0 +1,19 @@
+{
+  stdenv,
+  fetchFromGitHub,
+  autoreconfHook,
+  zlib,
+}:
+stdenv.mkDerivation rec {
+  name = "quip";
+
+  src = fetchFromGitHub {
+    owner = "dcjones";
+    repo = "quip";
+    rev = "9165bb5ac17a2cf2822e437df573487d7adfa1cc";
+    sha256 = "PpvgLzdiYcLyJ1JH9UzbUd29eKIlyY440HiJGYWvkrs=";
+  };
+
+  nativeBuildInputs = [autoreconfHook];
+  buildInputs = [zlib];
+}
diff --git a/tools/quip-quip.nix b/tools/quip-quip.nix
new file mode 100644
index 0000000..77cf557
--- /dev/null
+++ b/tools/quip-quip.nix
@@ -0,0 +1,17 @@
+{bionix}:
+with bionix;
+with lib.types;
+  input: let
+    ref = matchFiletype "quip" {bam = f: f.ref;} input;
+  in
+    stage {
+      name = "quip";
+      buildInputs = [quip.app];
+      buildCommand = ''
+        ln -s ${input} input.bam
+        quip -r ${ref} input.bam
+        cp input.bam.qp $out
+      '';
+      stripStorePaths = false;
+      passthru.filetype = filetype.qp input.filetype;
+    }
diff --git a/tools/quip-unquip.nix b/tools/quip-unquip.nix
new file mode 100644
index 0000000..8c9cc01
--- /dev/null
+++ b/tools/quip-unquip.nix
@@ -0,0 +1,18 @@
+{bionix}:
+with bionix;
+with lib.types;
+  input: let
+    bamft = matchFiletype "unquip" {qp = x: x;} input;
+    ref = matchFiletype' "unquip-sub" {bam = f: f.ref;} bamft;
+  in
+    stage {
+      name = "unquip";
+      buildInputs = [quip.app];
+      buildCommand = ''
+        ln -s ${input} input.bam.qp
+        unquip -r ${ref} input.bam.qp
+        cp input.bam $out
+      '';
+      stripStorePaths = false;
+      passthru.filetype = bamft;
+    }
diff --git a/tools/quip.nix b/tools/quip.nix
new file mode 100644
index 0000000..f0a57aa
--- /dev/null
+++ b/tools/quip.nix
@@ -0,0 +1,6 @@
+{bionix}:
+with bionix; {
+  app = pkgs.callPackage ./quip-app.nix {};
+  quip = callBionix ./quip-quip.nix;
+  unquip = callBionix ./quip-unquip.nix;
+}
-- 
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