From 2ada3b5d3e4d776fc1e5dcdc1c34a4b7bd884614 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Tue, 17 Dec 2019 14:26:28 +1100
Subject: [PATCH 1/3] samblaster: init 0.1.24
---
.../science/biology/samblaster/default.nix | 26 +++++++++++++++++++
pkgs/top-level/all-packages.nix | 2 ++
2 files changed, 28 insertions(+)
create mode 100644 pkgs/applications/science/biology/samblaster/default.nix
diff --git a/pkgs/applications/science/biology/samblaster/default.nix b/pkgs/applications/science/biology/samblaster/default.nix
new file mode 100644
index 00000000000..7795ba23736
--- /dev/null
+++ b/pkgs/applications/science/biology/samblaster/default.nix
@@ -0,0 +1,26 @@
+{ stdenv, fetchFromGitHub }:
+
+stdenv.mkDerivation rec {
+ pname = "samblaster";
+ version = "0.1.24";
+
+ src = fetchFromGitHub {
+ owner = "GregoryFaust";
+ repo = "samblaster";
+ rev = "v.${version}";
+ sha256 = "0iv2ddfw8363vb2x8gr3p8g88whb6mb9m0pf71i2cqsbv6jghap7";
+ };
+
+ installPhase = ''
+ mkdir -p $out/bin
+ cp samblaster $out/bin
+ '';
+
+ meta = with stdenv.lib; {
+ description = "Tool for marking duplicates and extracting discordant/split reads from SAM/BAM files";
+ maintainers = with maintainers; [ jbedo ];
+ license = licenses.mit;
+ homepage = "https://github.com/GregoryFaust/samblaster";
+ platforms = platforms.x86_64;
+ };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index f635f7a81eb..f2225ac2430 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -24919,6 +24919,8 @@ in
mpi = true;
});
+ samblaster = callPackage ../applications/science/biology/samblaster { };
+
samtools = callPackage ../applications/science/biology/samtools { };
samtools_0_1_19 = callPackage ../applications/science/biology/samtools/samtools_0_1_19.nix {
stdenv = gccStdenv;
From 617483d27a35247e1fbd8bcb9596a64d74fc4e28 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 18 Dec 2019 08:54:44 +1100
Subject: [PATCH 2/3] sambamba: init 0.7.1
---
.../science/biology/sambamba/default.nix | 31 +++++++++++++++++++
pkgs/top-level/all-packages.nix | 2 ++
2 files changed, 33 insertions(+)
create mode 100644 pkgs/applications/science/biology/sambamba/default.nix
diff --git a/pkgs/applications/science/biology/sambamba/default.nix b/pkgs/applications/science/biology/sambamba/default.nix
new file mode 100644
index 00000000000..7e33a661218
--- /dev/null
+++ b/pkgs/applications/science/biology/sambamba/default.nix
@@ -0,0 +1,31 @@
+{ stdenv, fetchFromGitHub, python3, which, dmd, ldc, zlib }:
+
+stdenv.mkDerivation rec {
+ pname = "sambamba";
+ version = "0.7.1";
+
+ src = fetchFromGitHub {
+ owner = "biod";
+ repo = "sambamba";
+ rev = "v${version}";
+ sha256 = "0k5wy06zrbsc40x6answgz7rz2phadyqwlhi9nqxbfqanbg9kq20";
+ fetchSubmodules = true;
+ };
+
+ nativeBuildInputs = [ which python3 dmd ldc ];
+ buildInputs = [ zlib ];
+
+ # Upstream's install target is broken; copy manually
+ installPhase = ''
+ mkdir -p $out/bin
+ cp bin/sambamba-${version} $out/bin/sambamba
+ '';
+
+ meta = with stdenv.lib; {
+ description = "SAM/BAM processing tool";
+ homepage = "https://lomereiter.github.io/sambamba/";
+ maintainers = with maintainers; [ jbedo ];
+ license = with licenses; gpl2;
+ platforms = platforms.x86_64;
+ };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index f2225ac2430..d1a0d7d384e 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -24919,6 +24919,8 @@ in
mpi = true;
});
+ sambamba = callPackage ../applications/science/biology/sambamba { };
+
samblaster = callPackage ../applications/science/biology/samblaster { };
samtools = callPackage ../applications/science/biology/samtools { };
From a3d6e7b4b4585c5bc5bd8c7e6c8f305daecdd03b Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 18 Dec 2019 09:37:39 +1100
Subject: [PATCH 3/3] lumpy: init 0.3.0
---
.../science/biology/lumpy/default.nix | 47 +++++++++++++++++++
pkgs/top-level/all-packages.nix | 2 +
2 files changed, 49 insertions(+)
create mode 100644 pkgs/applications/science/biology/lumpy/default.nix
diff --git a/pkgs/applications/science/biology/lumpy/default.nix b/pkgs/applications/science/biology/lumpy/default.nix
new file mode 100644
index 00000000000..04512e8e372
--- /dev/null
+++ b/pkgs/applications/science/biology/lumpy/default.nix
@@ -0,0 +1,47 @@
+{ stdenv, fetchFromGitHub, htslib, zlib, curl, openssl, samblaster, sambamba
+, samtools, hexdump, python2Packages, which }:
+
+let
+ python =
+ python2Packages.python.withPackages (pkgs: with pkgs; [ pysam numpy ]);
+
+in stdenv.mkDerivation rec {
+ pname = "lumpy";
+ version = "0.3.0";
+
+ src = fetchFromGitHub {
+ owner = "arq5x";
+ repo = "lumpy-sv";
+ rev = version;
+ sha256 = "0azhzvmh9az9jcq0xprlzdz6w16azgszv4kshb903bwbnqirmk18";
+ };
+
+ nativeBuildInputs = [ which ];
+ buildInputs =
+ [ htslib zlib curl openssl python samblaster sambamba samtools hexdump ];
+
+ preConfigure = ''
+ patchShebangs ./.
+
+ # Use Nix htslib over bundled version
+ sed -i 's/lumpy_filter: htslib/lumpy_filter:/' Makefile
+ sed -i 's|../../lib/htslib/libhts.a|-lhts|' src/filter/Makefile
+ '';
+
+ # Upstream's makefile doesn't have an install target
+ installPhase = ''
+ mkdir -p $out
+ cp -r bin $out
+ cp -r scripts $out
+ sed -i 's|/build/source|'$out'|' $out/bin/lumpyexpress.config
+ '';
+
+ meta = with stdenv.lib; {
+ description = "Probabilistic structural variant caller";
+ homepage = "https://github.com/arq5x/lumpy-sv";
+ maintainers = with maintainers; [ jbedo ];
+ license = licenses.mit;
+ platforms = [ "x86_64-linux" ];
+ };
+
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index d1a0d7d384e..e0e54e1da95 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -24845,6 +24845,8 @@ in
last = callPackage ../applications/science/biology/last { };
+ lumpy = callPackage ../applications/science/biology/lumpy { };
+
macse = callPackage ../applications/science/biology/macse { };
migrate = callPackage ../applications/science/biology/migrate { };