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authorJustin Bedo <cu@cua0.org>2021-08-25 10:01:58 +1000
committerJustin Bedo <cu@cua0.org>2021-08-25 10:01:58 +1000
commit73f249f6e6ab181e71464a9f305ca13656ebf901 (patch)
treea8298e9e0d1d4aeeb51cdac70f1510a32207aba3
parentbc5709e934bbe1d477764fe153a198ccc669e6bb (diff)
fastp: use nixpkgs version
-rw-r--r--tools/fastp-app.nix23
-rw-r--r--tools/fastp-check.nix2
-rw-r--r--tools/fastp.nix2
3 files changed, 1 insertions, 26 deletions
diff --git a/tools/fastp-app.nix b/tools/fastp-app.nix
deleted file mode 100644
index bb716e2..0000000
--- a/tools/fastp-app.nix
+++ /dev/null
@@ -1,23 +0,0 @@
-{ stdenv
-, fetchFromGitHub
-, zlib
-}:
-
-stdenv.mkDerivation rec {
- name = "fastp-${version}";
- version = "0.20.0";
-
- src = fetchFromGitHub {
- owner = "OpenGene";
- repo = "fastp";
- rev = "v${version}";
- sha256 = "0y0qfp3j3gqnmlqskna8x43acss21vxwck287c4fagxlcaba0s30";
- };
-
- buildInputs = [ zlib ];
-
- installPhase = ''
- mkdir -p $out/bin
- cp fastp $out/bin
- '';
-}
diff --git a/tools/fastp-check.nix b/tools/fastp-check.nix
index bd522d8..06f00ae 100644
--- a/tools/fastp-check.nix
+++ b/tools/fastp-check.nix
@@ -16,7 +16,7 @@ let
out =
stage {
name = "fastp";
- buildInputs = [ fastp.app ];
+ buildInputs = [ pkgs.fastp ];
outputs = [ "out" "fastq1" "json" ] ++ (if input2 != null then [ "fastq2" ] else []);
buildCommand = ''
mkdir -p $out
diff --git a/tools/fastp.nix b/tools/fastp.nix
index 551d270..36bc690 100644
--- a/tools/fastp.nix
+++ b/tools/fastp.nix
@@ -3,8 +3,6 @@
with bionix;
rec {
- app = pkgs.callPackage ./fastp-app.nix {};
-
/* Check and filter fastqs
Type: { ... } -> { input1, input2 ? null } -> { out :: html, fastq1 :: fastq, fastq2 :: fastq, json :: JSON }
*/