From fde6c31445e72cfc976971e6811bb5c84d0cf679 Mon Sep 17 00:00:00 2001
From: Armin Sobhani <asobhani@sharcnet.ca>
Date: Tue, 8 May 2018 16:57:14 -0400
Subject: [PATCH] add idba bioinformatics package

---
 .version              |  2 +-
 pkgs/all-packages.nix |  2 ++
 pkgs/idba.nix         | 37 +++++++++++++++++++++++++++++++++++++
 3 files changed, 40 insertions(+), 1 deletion(-)
 create mode 100644 pkgs/idba.nix

diff --git a/.version b/.version
index 2fdad9f..a88d2ca 100644
--- a/.version
+++ b/.version
@@ -1 +1 @@
-17.09
+18.03
diff --git a/pkgs/all-packages.nix b/pkgs/all-packages.nix
index d8bc318..3f5e418 100644
--- a/pkgs/all-packages.nix
+++ b/pkgs/all-packages.nix
@@ -34,6 +34,8 @@ self: super: pkgs: with pkgs; {
 
   sambamba = callPackage ./sambamba { };
 
+  idba = callPackage ./idba.nix { };
+
   nixStable = super.nixStable.overrideAttrs
     ( attrs: { patches = attrs.patches or [] ++ [ ./nix/remote.patch ./nix/cvmfs.patch ]; } );
   nix = super.nix.overrideAttrs
diff --git a/pkgs/idba.nix b/pkgs/idba.nix
new file mode 100644
index 0000000..f49f42e
--- /dev/null
+++ b/pkgs/idba.nix
@@ -0,0 +1,37 @@
+{ stdenv, fetchurl
+, bash }:
+
+stdenv.mkDerivation rec {
+  version = "1.1.3";
+  name = "idba-${version}";
+
+  src = fetchurl {
+    url = "https://github.com/loneknightpy/idba/releases/download/${version}/idba-${version}.tar.gz";
+    sha256 = "1l16mvxyr226gzrd0kw423im2nv07dvvzaib40f5qwkd7i3283h3";
+  };
+
+  # increase max sequence length to 256 
+  postPatch = ''
+    sed -i 's/kMaxShortSequence = 128/kMaxShortSequence = 256/' src/sequence/short_sequence.h
+  '';
+
+  # default 'make install' has a bug that doesn't install all the binaries
+  installPhase = ''
+    mkdir -p $out/bin
+    find ./bin -maxdepth 1 -type f -perm /a+x -exec cp -av {} $out/bin \;
+  '';
+
+  # buildInputs = [
+  #   stdenv
+  # ];
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/loneknightpy/idba/;
+    description = "Basic iterative de Bruijn graph assembler for second-generation sequencing reads";
+    longDescription = "IDBA is the basic iterative de Bruijn graph assembler for second-generation sequencing reads. IDBA-UD, an extension of IDBA, is designed to utilize paired-end reads to assemble low-depth regions and use progressive depth on contigs to reduce errors in high-depth regions. It is a generic purpose assembler and especially good for single-cell and metagenomic sequencing data. IDBA-Hybrid is another update version of IDBA-UD, which can make use of a similar reference genome to improve assembly result. IDBA-Tran is an iterative de Bruijn graph assembler for RNA-Seq data.";
+    platforms = platforms.all;
+    license = licenses.gpl3;
+  };
+
+  enableParallelBuilding = true;
+}