commit 7726aa9ce610dd80bfcfb6983ba817cd05aba46e · pyrox.dev/nixpkgs

+56

pkgs/applications/science/biology/tandem-aligner/default.nix

···

       1
       1
       +
       { lib

     

       2
       2
       +
       , stdenv

     

       3
       3
       +
       , fetchFromGitHub

     

       4
       4
       +
       , cmake

     

       5
       5
       +
       , zlib

     

       6
       6
       +
       }:

     

       7
       7
       +
       

     

       8
       8
       +
       stdenv.mkDerivation {

     

       9
       9
       +
         pname = "TandemAligner";

     

       10
       10
       +
         version = "unstable-2022-09-17";

     

       11
       11
       +
       

     

       12
       12
       +
         src = fetchFromGitHub {

     

       13
       13
       +
           owner = "seryrzu";

     

       14
       14
       +
           repo = "tandem_aligner";

     

       15
       15
       +
           rev = "ac6004f108ad20477045f4d0b037d96051a9df70";

     

       16
       16
       +
           hash = "sha256-iMDj1HZ8LzmZckuAM3lbG3eSJSd/5JGVA6SBs7+AgX8=";

     

       17
       17
       +
         };

     

       18
       18
       +
       

     

       19
       19
       +
         sourceRoot = "source/tandem_aligner";

     

       20
       20
       +
       

     

       21
       21
       +
         nativeBuildInputs = [ cmake ];

     

       22
       22
       +
       

     

       23
       23
       +
         buildInputs = [ zlib ];

     

       24
       24
       +
       

     

       25
       25
       +
         installPhase = ''

     

       26
       26
       +
           runHook preInstall

     

       27
       27
       +
           mkdir -p $out/bin

     

       28
       28
       +
           cp src/projects/tandem_aligner/tandem_aligner $out/bin

     

       29
       29
       +
           runHook postInstall

     

       30
       30
       +
         '';

     

       31
       31
       +
       

     

       32
       32
       +
         doCheck = true;

     

       33
       33
       +
       

     

       34
       34
       +
         # adapted from target test_launch in Makefile

     

       35
       35
       +
         checkPhase = ''

     

       36
       36
       +
           runHook preCheck

     

       37
       37
       +
           mkdir -p $TMPDIR/test_launch

     

       38
       38
       +
           src/projects/tandem_aligner/tandem_aligner \

     

       39
       39
       +
             --first $src/tandem_aligner/test_dataset/first.fasta \

     

       40
       40
       +
             --second $src/tandem_aligner/test_dataset/second.fasta \

     

       41
       41
       +
             -o $TMPDIR/test_launch \

     

       42
       42
       +
             --debug

     

       43
       43
       +
           grep -q "Thank you for using TandemAligner!" $TMPDIR/test_launch/tandem_aligner.log

     

       44
       44
       +
           diff $TMPDIR/test_launch/cigar.txt $src/tandem_aligner/test_dataset/true_cigar.txt

     

       45
       45
       +
           runHook postCheck

     

       46
       46
       +
         '';

     

       47
       47
       +
       

     

       48
       48
       +
         meta = {

     

       49
       49
       +
           description = "A parameter-free algorithm for sequence alignment";

     

       50
       50
       +
           homepage = "https://github.com/seryrzu/tandem_aligner";

     

       51
       51
       +
           license = lib.licenses.bsd3;

     

       52
       52
       +
           maintainers = with lib.maintainers; [ amesgen ];

     

       53
       53
       +
           platforms = lib.platforms.linux;

     

       54
       54
       +
           mainProgram = "tandem_aligner";

     

       55
       55
       +
         };

     

       56
       56
       +
       }

pkgs/top-level/all-packages.nix

···

       36014
       36014
        
       

     

       36015
       36015
        
         svaba = callPackage ../applications/science/biology/svaba { };

     

       36016
       36016
        
       

     

       36017
       36017
       +
         tandem-aligner = callPackage ../applications/science/biology/tandem-aligner { };

     

       36018
       36018
       +
       

     

       36017
       36019
        
         tebreak = callPackage ../applications/science/biology/tebreak { };

     

       36018
       36020
        
       

     

       36019
       36021
        
         treemix = callPackage ../applications/science/biology/treemix { };