pyrox.dev
1{
2 lib,
3 buildPerlPackage,
4 fetchFromGitHub,
5}:
6
7buildPerlPackage rec {
8 pname = "BioExtAlign";
9 version = "1.5.1";
10
11 outputs = [ "out" ];
12
13 src = fetchFromGitHub {
14 owner = "bioperl";
15 repo = "bioperl-ext";
16 rev = "bioperl-ext-release-${lib.replaceStrings [ "." ] [ "-" ] version}";
17 sha256 = "sha256-+0tZ6q3PFem8DWa2vq+njOLmjDvMB0JhD0FGk00lVMA=";
18 };
19
20 patches = [
21 # Starting for Perl 5.6, implicit function declaration are treated as errors
22 # There may be an error but ensembl-vep (the main package for this dependency)
23 # runs
24 ./no-implicit-function.patch
25 # Tests need other parts of BioExt, disabling them
26 ./disable-other-tests.patch
27 ./fprintf.patch
28 ];
29
30 # Do not install other Bio-ext packages
31 preConfigure = ''
32 cd Bio/Ext/Align
33 '';
34
35 # Disable tests as it requires Bio::Tools::Align which is in a different directory
36 buildPhase = ''
37 make
38 '';
39
40 checkPhase = ''
41 runHook preCheck
42
43 make test
44
45 runHook postCheck
46 '';
47
48 meta = {
49 homepage = "https://github.com/bioperl/bioperl-ext";
50 description = "Write Perl Subroutines in Other Programming Languages";
51 longDescription = ''
52 Part of BioPerl Extensions (BioPerl-Ext) distribution, a collection of Bioperl C-compiled extensions.
53 '';
54 license = with lib.licenses; [ artistic1 ];
55 maintainers = with lib.maintainers; [ apraga ];
56 };
57}