From b029bff0ec25ec06758a5fdf7c79152d2ed5c032 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Fri, 4 Jan 2019 11:37:38 +1100
Subject: snpeff: init

---
 tools/snpeff-annotate.nix | 21 +++++++++++++++++++++
 tools/snpeff-dbnsfp.nix   | 22 ++++++++++++++++++++++
 tools/snpeff.nix          |  8 ++++++++
 3 files changed, 51 insertions(+)
 create mode 100644 tools/snpeff-annotate.nix
 create mode 100644 tools/snpeff-dbnsfp.nix
 create mode 100644 tools/snpeff.nix

(limited to 'tools')

diff --git a/tools/snpeff-annotate.nix b/tools/snpeff-annotate.nix
new file mode 100644
index 0000000..a119c3c
--- /dev/null
+++ b/tools/snpeff-annotate.nix
@@ -0,0 +1,21 @@
+{bionix
+,nixpkgs
+,db
+,flags ? ""}:
+
+input:
+
+with nixpkgs;
+with bionix.types;
+
+assert (matchFiletype "snpeff-annotate" { vcf = _: true; } input);
+
+stdenv.mkDerivation {
+  name = "snpeff-annotate";
+  buildCommand = ''
+    ln -s ${db} ${db.name}
+    snpeff -nodownload -dataDir $TMPDIR ${db.name} ${input} > $out
+  '';
+  buildInputs = [ snpeff ];
+  passthru.filetype = input.filetype;
+}
diff --git a/tools/snpeff-dbnsfp.nix b/tools/snpeff-dbnsfp.nix
new file mode 100644
index 0000000..f9fbdaa
--- /dev/null
+++ b/tools/snpeff-dbnsfp.nix
@@ -0,0 +1,22 @@
+{bionix
+,nixpkgs
+,dbnsfp
+,flags ? ""}:
+
+input:
+
+with nixpkgs;
+with bionix.types;
+
+assert (matchFiletype "snpeff-dbnsfp" { vcf = _: true; } input);
+
+stdenv.mkDerivation {
+  name = "snpeff-dbnsfp";
+  buildCommand = ''
+    ln -s ${dbnsfp.db} dbNSFP.txt.gz
+    ln -s ${dbnsfp.index} dbNSFP.txt.gz.tbi
+    snpeff dbnsfp -db dbNSFP.txt.gz ${input} > $out
+  '';
+  buildInputs = [ snpeff ];
+  passthru.filetype = input.filetype;
+}
diff --git a/tools/snpeff.nix b/tools/snpeff.nix
new file mode 100644
index 0000000..2df8056
--- /dev/null
+++ b/tools/snpeff.nix
@@ -0,0 +1,8 @@
+{bionix, nixpkgs}:
+
+with bionix;
+
+{
+  annotate = callBionixE ./snpeff-annotate.nix;
+  dbnsfp = callBionixE ./snpeff-dbnsfp.nix;
+}
-- 
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