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| author | Alexis Praga <alexis.praga@free.fr> | 2022-08-13 16:49:20 +0000 |
|---|---|---|
| committer | Alexis Praga <alexis.praga@proton.me> | 2022-10-20 23:18:32 +0200 |
| commit | 02ff423121c4a3dc62edc4c51b2a48f03e95598f (patch) | |
| tree | 6bbf9a0a3dbe0150b9dbb669508efc9f78c54ab9 | |
| parent | f77a8a1df0cb83542be93f7d7ae962ab5a3ee78b (diff) | |
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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 These are no longer maintained but needed for Ensembl-VEP (annotation for genomics).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>
| -rw-r--r-- | pkgs/development/perl-modules/Bio-Ext-Align/default.nix | 36 | ||||
| -rw-r--r-- | pkgs/development/perl-modules/Bio-Ext-Align/fprintf.patch | 13 | ||||
| -rw-r--r-- | pkgs/top-level/perl-packages.nix | 2 |
3 files changed, 51 insertions, 0 deletions
diff --git a/pkgs/development/perl-modules/Bio-Ext-Align/default.nix b/pkgs/development/perl-modules/Bio-Ext-Align/default.nix new file mode 100644 index 00000000000..237a4be0361 --- /dev/null +++ b/pkgs/development/perl-modules/Bio-Ext-Align/default.nix @@ -0,0 +1,36 @@ +{ lib, buildPerlPackage, fetchFromGitHub }: + +buildPerlPackage rec { + pname = "BioExtAlign"; + version = "1.5.1"; + + outputs = [ "out" "dev" ]; + + src = fetchFromGitHub { + owner = "bioperl"; + repo = "bioperl-ext"; + rev = "bioperl-ext-release-${lib.replaceStrings ["."] ["-"] version}"; + sha256 = "sha256-+0tZ6q3PFem8DWa2vq+njOLmjDvMB0JhD0FGk00lVMA="; + }; + + patches = [ ./fprintf.patch ]; + + # Do not install other Bio-ext packages + preConfigure = '' + cd Bio/Ext/Align + ''; + + # Disable tests as it requires Bio::Tools::Align which is in a different directory + buildPhase = '' + make + ''; + + meta = { + homepage = "https://github.com/bioperl/bioperl-ext"; + description = "Write Perl Subroutines in Other Programming Languages"; + longDescription = '' + Part of BioPerl Extensions (BioPerl-Ext) distribution, a collection of Bioperl C-compiled extensions. + ''; + license = with lib.licenses; [ artistic1 ]; + }; +} diff --git a/pkgs/development/perl-modules/Bio-Ext-Align/fprintf.patch b/pkgs/development/perl-modules/Bio-Ext-Align/fprintf.patch new file mode 100644 index 00000000000..f62004a9a33 --- /dev/null +++ b/pkgs/development/perl-modules/Bio-Ext-Align/fprintf.patch @@ -0,0 +1,13 @@ +diff --git a/libs/dpalign.c b/libs/dpalign.c +index 0e07b67..0eab932 100644 +--- a/Bio/Ext/Align/libs/dpalign.c ++++ b/Bio/Ext/Align/libs/dpalign.c +@@ -40,7 +40,7 @@ int blosum62[24][24] = { + void + dpAlign_fatal(char * s) + { +- fprintf(stderr, s); ++ fputs(stderr, s); + exit(-1); + } + diff --git a/pkgs/top-level/perl-packages.nix b/pkgs/top-level/perl-packages.nix index 73a753bae29..f71f736a697 100644 --- a/pkgs/top-level/perl-packages.nix +++ b/pkgs/top-level/perl-packages.nix @@ -1594,6 +1594,8 @@ let }; }; + BioExtAlign = callPackage ../development/perl-modules/Bio-Ext-Align { }; + BioPerl = buildPerlPackage { pname = "BioPerl"; version = "1.7.8"; |