From 13a1f2c296efd872a4ff9720be34e1a28700a075 Mon Sep 17 00:00:00 2001 From: Luis Pedro Coelho Date: Mon, 15 Apr 2019 08:22:47 +0800 Subject: [PATCH] eggnog-mapper: init at 1.0.3 (#58905) --- .../science/biology/eggnog-mapper/default.nix | 40 +++++++++++++++++++ pkgs/top-level/all-packages.nix | 2 + 2 files changed, 42 insertions(+) create mode 100644 pkgs/applications/science/biology/eggnog-mapper/default.nix diff --git a/pkgs/applications/science/biology/eggnog-mapper/default.nix b/pkgs/applications/science/biology/eggnog-mapper/default.nix new file mode 100644 index 00000000000..a15425ec213 --- /dev/null +++ b/pkgs/applications/science/biology/eggnog-mapper/default.nix @@ -0,0 +1,40 @@ +{ stdenv, fetchFromGitHub, fetchpatch, makeWrapper, python27Packages, wget, diamond, hmmer }: + +python27Packages.buildPythonApplication rec { + pname = "eggnog-mapper"; + version = "1.0.3"; + + src = fetchFromGitHub { + owner = "eggnogdb"; + repo = "eggnog-mapper"; + rev = "${version}"; + sha256 = "1aaaflppy84bhkh2hb5gnzm4xgrz0rz0cgfpadr9w8cva8p0sqdv"; + }; + + patches = (fetchpatch { + url = https://github.com/eggnogdb/eggnog-mapper/pull/125/commits/b7828e4c8c1c453e391aef050f06ff3f84ff9faf.patch; + sha256 = "0nz1a7ybm4j5c7vdm3annnxz9036iam2044hia341a0am9wydmzk"; + }); + + buildInputs = [ makeWrapper ]; + propagatedBuildInputs = [ python27Packages.biopython wget diamond hmmer ]; + + # make emapper find diamond & hmmer + makeWrapperArgs = [ + ''--prefix PATH ':' "${diamond}/bin"'' + ''--prefix PATH ':' "${hmmer}/bin"'' + ]; + + # Tests rely on some of the databases being available, which is not bundled + # with this package as (1) in total, they represent >100GB of data, and (2) + # the user can download only those that interest them. + doCheck = false; + + meta = with stdenv.lib; { + description = "Fast genome-wide functional annotation through orthology assignment"; + license = licenses.gpl2; + homepage = https://github.com/eggnogdb/eggnog-mapper/wiki; + maintainers = with maintainers; [ luispedro ]; + platforms = platforms.all; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 3a37d96330a..13e7382f6cd 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -21828,6 +21828,8 @@ in ecopcr = callPackage ../applications/science/biology/ecopcr { }; + eggnog-mapper = callPackage ../applications/science/biology/eggnog-mapper { }; + emboss = callPackage ../applications/science/biology/emboss { }; ezminc = callPackage ../applications/science/biology/EZminc { };