68 lines
1.8 KiB
Nix
68 lines
1.8 KiB
Nix
{ lib
|
|
, stdenv
|
|
, fetchFromGitHub
|
|
, fetchpatch
|
|
, cmake
|
|
, zlib
|
|
}:
|
|
|
|
stdenv.mkDerivation (finalAttrs: {
|
|
pname = "TandemAligner";
|
|
version = "0.1";
|
|
|
|
src = fetchFromGitHub {
|
|
owner = "seryrzu";
|
|
repo = "tandem_aligner";
|
|
rev = "v${finalAttrs.version}";
|
|
hash = "sha256-iMDj1HZ8LzmZckuAM3lbG3eSJSd/5JGVA6SBs7+AgX8=";
|
|
};
|
|
|
|
patches = [
|
|
(fetchpatch {
|
|
# https://github.com/seryrzu/tandem_aligner/pull/4
|
|
url = "https://github.com/seryrzu/tandem_aligner/commit/8b516c94f90aaa9cb84278aa811285d4204b03a9.patch";
|
|
hash = "sha256-kD46SykXklG/avK0+sc61YKFw9Bes8ZgFAjVXmcpN8k=";
|
|
stripLen = 1;
|
|
})
|
|
];
|
|
|
|
sourceRoot = "${finalAttrs.src.name}/tandem_aligner";
|
|
|
|
nativeBuildInputs = [ cmake ];
|
|
|
|
buildInputs = [ zlib ];
|
|
|
|
installPhase = ''
|
|
runHook preInstall
|
|
mkdir -p $out/bin
|
|
cp src/projects/tandem_aligner/tandem_aligner $out/bin
|
|
runHook postInstall
|
|
'';
|
|
|
|
doCheck = true;
|
|
|
|
# adapted from target test_launch in Makefile
|
|
checkPhase = ''
|
|
runHook preCheck
|
|
mkdir -p $TMPDIR/test_launch
|
|
src/projects/tandem_aligner/tandem_aligner \
|
|
--first $src/tandem_aligner/test_dataset/first.fasta \
|
|
--second $src/tandem_aligner/test_dataset/second.fasta \
|
|
-o $TMPDIR/test_launch \
|
|
--debug
|
|
grep -q "Thank you for using TandemAligner!" $TMPDIR/test_launch/tandem_aligner.log
|
|
diff $TMPDIR/test_launch/cigar.txt $src/tandem_aligner/test_dataset/true_cigar.txt
|
|
runHook postCheck
|
|
'';
|
|
|
|
meta = {
|
|
description = "A parameter-free algorithm for sequence alignment";
|
|
homepage = "https://github.com/seryrzu/tandem_aligner";
|
|
changelog = "https://github.com/seryrzu/tandem_aligner/releases/tag/v${finalAttrs.version}";
|
|
license = lib.licenses.bsd3;
|
|
maintainers = with lib.maintainers; [ amesgen ];
|
|
platforms = lib.platforms.linux;
|
|
mainProgram = "tandem_aligner";
|
|
};
|
|
})
|