commit 386d93d06d1789d1bdfbd944afbe285213cb4ce8 · pyrox.dev/nixpkgs

+20 -5

pkgs/development/perl-modules/Bio-Ext-Align/default.nix

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         pname = "BioExtAlign";

     

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         version = "1.5.1";

     

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         outputs = [

     

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           "out"

     

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           "dev"

     

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       -
         ];

     

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         outputs = [ "out" ];

     

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         src = fetchFromGitHub {

     

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           owner = "bioperl";

     
···

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           sha256 = "sha256-+0tZ6q3PFem8DWa2vq+njOLmjDvMB0JhD0FGk00lVMA=";

     

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         };

     

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         patches = [ ./fprintf.patch ];

     

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         patches = [

     

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           # Starting for Perl 5.6, implicit function declaration are treated as errors

     

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           # There may be an error but ensembl-vep (the main package for this dependency)

     

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           # runs

     

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           ./no-implicit-function.patch

     

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           # Tests need other parts of BioExt, disabling them

     

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           ./disable-other-tests.patch

     

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           ./fprintf.patch

     

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         ];

     

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         # Do not install other Bio-ext packages

     

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         preConfigure = ''

     
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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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         checkPhase = ''

     

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           runHook preCheck

     

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           make test

     

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           runHook postCheck

     

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         '';

     

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         meta = {

     
···

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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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           maintainers = with lib.maintainers; [ apraga ];

     

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         };

     

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       }

+84

pkgs/development/perl-modules/Bio-Ext-Align/disable-other-tests.patch

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       diff --git a/Bio/Ext/Align/test.pl b/Bio/Ext/Align/test.pl

     

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       index 72411f3..1deb77b 100755

     

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       --- a/Bio/Ext/Align/test.pl

     

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       +++ b/Bio/Ext/Align/test.pl

     

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       @@ -8,13 +8,10 @@ my $DEBUG = $ENV{'BIOPERLDEBUG'} || 0;

     

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        BEGIN {

     

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            eval { require Test; };

     

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            use Test;

     

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       -    plan tests => 9;

     

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       +    plan tests => 4;

     

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        }

     

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        use Bio::Ext::Align;

     

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       -use Bio::Tools::dpAlign;

     

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       -use Bio::Seq;

     

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       -use Bio::AlignIO;

     

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        $loaded = 1;

     

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        ok(1); # modules loaded

     

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       @@ -34,64 +31,3 @@ $alb = &Bio::Ext::Align::Align_Sequences_ProteinSmithWaterman($seq1,$seq2,

     

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        					 $seq2->seq,15,50,STDERR) if $DEBUG;

     

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       -warn( "Testing Local Alignment case...\n") if $DEBUg;

     

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       -

     

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       -$alnout = new Bio::AlignIO(-format => 'pfam', -fh => \*STDERR);

     

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       -$aln = &Bio::Ext::Align::Align_DNA_Sequences("AATGCCATTGACGG",

     

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       -					     "CAGCCTCGCTTAG",3,-1,3,1,

     

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       -		      Bio::Tools::dpAlign::DPALIGN_LOCAL_MILLER_MYERS);

     

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       -

     

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       -$out = Bio::SimpleAlign->new();

     

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       -

     

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       -$out->add_seq(Bio::LocatableSeq->new(-seq   => $aln->aln1,

     

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       -				     -start => $aln->start1,

     

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       -				     -end   => $aln->end1,

     

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       -				     -id    => "one"));

     

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       -

     

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       -$out->add_seq(Bio::LocatableSeq->new(-seq   => $aln->aln2,

     

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       -				     -start => $aln->start2,

     

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       -				     -end   => $aln->end2,

     

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       -				     -id    => "two"));

     

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       -$alnout->write_aln($out) if $DEBUG;

     

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       -

     

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       -$aln = &Bio::Ext::Align::Align_Protein_Sequences("WLGQRNLVSSTGGNLLNVWLKDW","WMGNRNVVNLLNVWFRDW",0,

     

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       -						 Bio::Tools::dpAlign::DPALIGN_LOCAL_MILLER_MYERS);

     

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       -$out = Bio::SimpleAlign->new();

     

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       -ok($aln);

     

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       -

     

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       -$out->add_seq(Bio::LocatableSeq->new(-seq   => $aln->aln1,

     

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       -				     -start => $aln->start1,

     

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       -				     -end   => $aln->end1,

     

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       -				     -id    => "one"));

     

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       -

     

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       -$out->add_seq(Bio::LocatableSeq->new(-seq   => $aln->aln2,

     

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       -				     -start => $aln->start2,

     

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       -				     -end   => $aln->end2,

     

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       -				     -id    => "two"));

     

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       -$alnout->write_aln($out) if $DEBUG;

     

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       -ok(1);

     

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       -

     

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       -warn( "Testing Global Alignment case...\n") if $DEBUG;

     

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       -

     

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       -$factory = new Bio::Tools::dpAlign('-alg' => Bio::Tools::dpAlign::DPALIGN_GLOBAL_MILLER_MYERS);

     

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       -$s1 = new Bio::Seq(-id => "one", -seq => "AATGCCATTGACGG", -alphabet => 'dna');

     

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       -$s2 = new Bio::Seq(-id => "two", -seq => "CAGCCTCGCTTAG", -alphabet => 'dna');

     

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       -$aln = $factory->pairwise_alignment($s1, $s2);

     

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       -$alnout->write_aln($aln) if $DEBUG;

     

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       -$factory->align_and_show($s1, $s2) if $DEBUG;

     

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       -

     

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       -ok(1);

     

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       -

     

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       -$s1 = new Bio::Seq(-id => "one", -seq => "WLGQRNLVSSTGGNLLNVWLKDW", 

     

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       -		   -alphabet => 'protein');

     

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       -$s2 = new Bio::Seq(-id => "two", -seq => "WMGNRNVVNLLNVWFRDW", 

     

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       -		   -alphabet => 'protein');

     

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       -$aln = $factory->pairwise_alignment($s1, $s2);

     

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       -$alnout->write_aln($aln) if $DEBUG;

     

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       -$factory->align_and_show($s1, $s2) if $DEBUG;

     

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       -ok(1);

     

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       -

     

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       -$prof = $factory->sequence_profile($s1);

     

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       -warn( "Optimal Alignment Score = %d\n", $factory->pairwise_alignment_score($prof, $s2)) if $DEBUG;

     

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       -

     

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       -ok($factory->pairwise_alignment_score($prof,$s2),77);

+1 -1

pkgs/development/perl-modules/Bio-Ext-Align/fprintf.patch

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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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       +    fputs(s, stderr);

     

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            exit(-1);

     

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        }

     

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+13

pkgs/development/perl-modules/Bio-Ext-Align/no-implicit-function.patch

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       diff --git a/Bio/Ext/Align/Makefile.PL b/Bio/Ext/Align/Makefile.PL

     

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       index cc6c343..ea5cffa 100755

     

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       --- a/Bio/Ext/Align/Makefile.PL

     

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       +++ b/Bio/Ext/Align/Makefile.PL

     

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       @@ -5,7 +5,7 @@ WriteMakefile(

     

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            'NAME'	=> 'Bio::Ext::Align',

     

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            'VERSION'	=> '1.5.1',

     

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            'LIBS'	=> ['-lm'],   # e.g., '-lm' 

     

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       -    'DEFINE'	=> '-DPOSIX -DNOERROR',     # e.g., '-DHAVE_SOMETHING' 

     

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       +    'DEFINE'	=> '-DPOSIX -DNOERROR -Wno-implicit-function-declaration',     # e.g., '-DHAVE_SOMETHING'

     

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            'INC'	=> '-I./libs',     # e.g., '-I/usr/include/other'

     

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            'MYEXTLIB'  => 'libs/libsw$(LIB_EXT)',

     

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            'clean'     => { 'FILES' => 'libs/*.o libs/*.a' }