bioextalign: init at 1.5.1
Part of BioPerl Extensions (BioPerl-Ext) distribution, a collection of Bioperl C-compiled extensions. These are no longer maintained but needed for Ensembl-VEP (annotation for genomics). Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
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pkgs/development/perl-modules/Bio-Ext-Align/default.nix
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pkgs/development/perl-modules/Bio-Ext-Align/default.nix
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{ lib, buildPerlPackage, fetchFromGitHub }:
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buildPerlPackage rec {
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pname = "BioExtAlign";
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version = "1.5.1";
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outputs = [ "out" "dev" ];
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src = fetchFromGitHub {
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owner = "bioperl";
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repo = "bioperl-ext";
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rev = "bioperl-ext-release-${lib.replaceStrings ["."] ["-"] version}";
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sha256 = "sha256-+0tZ6q3PFem8DWa2vq+njOLmjDvMB0JhD0FGk00lVMA=";
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};
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patches = [ ./fprintf.patch ];
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# Do not install other Bio-ext packages
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preConfigure = ''
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cd Bio/Ext/Align
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'';
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# Disable tests as it requires Bio::Tools::Align which is in a different directory
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buildPhase = ''
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make
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'';
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meta = {
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homepage = "https://github.com/bioperl/bioperl-ext";
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description = "Write Perl Subroutines in Other Programming Languages";
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longDescription = ''
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Part of BioPerl Extensions (BioPerl-Ext) distribution, a collection of Bioperl C-compiled extensions.
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'';
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license = with lib.licenses; [ artistic1 ];
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};
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}
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13
pkgs/development/perl-modules/Bio-Ext-Align/fprintf.patch
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pkgs/development/perl-modules/Bio-Ext-Align/fprintf.patch
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diff --git a/libs/dpalign.c b/libs/dpalign.c
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index 0e07b67..0eab932 100644
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--- a/Bio/Ext/Align/libs/dpalign.c
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+++ b/Bio/Ext/Align/libs/dpalign.c
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@@ -40,7 +40,7 @@ int blosum62[24][24] = {
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void
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dpAlign_fatal(char * s)
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{
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- fprintf(stderr, s);
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+ fputs(stderr, s);
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exit(-1);
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}
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@ -1594,6 +1594,8 @@ let
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};
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};
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};
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};
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BioExtAlign = callPackage ../development/perl-modules/Bio-Ext-Align { };
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BioPerl = buildPerlPackage {
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BioPerl = buildPerlPackage {
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pname = "BioPerl";
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pname = "BioPerl";
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version = "1.7.8";
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version = "1.7.8";
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