Commit cc4bd303 authored by Alexis Praga's avatar Alexis Praga
Browse files

perlPackages.BioBigfile: init at 1.07 

Perl interface to manipulate BigWig and BigBeg files (for genomics)
This will be used to package VEP : uttps://www.ensembl.org/info/docs/tools/vep/script/vep_download.html

For that, only kent version 335 works at the moment.
For this commit, 2 commits for kent are needed
- e027a5d8 : packaging kent header
- 2b2c6f4c : enabling patches in kent
parent 2b2c6f4c

pkgs/applications/science/biology/kent/kent-utils.patch

0 → 100644
+27 −0
Original line number Diff line number Diff line 
--- ./src/utils/bigWigCat/makefile.orig	2023-03-27 14:03:01.585896516 +0000

+++ ./src/utils/bigWigCat/makefile	2023-03-27 14:03:27.716180479 +0000

@@ -1,3 +1,4 @@

 kentSrc = ../..

 A = bigWigCat

 include $(kentSrc)/inc/userApp.mk

+L += -lz



--- ./src/utils/pslLiftSubrangeBlat/makefile.orig	1970-01-01 00:00:01.000000000 +0000

+++ ./src/utils/pslLiftSubrangeBlat/makefile	2023-03-27 14:36:59.044600213 +0000

@@ -3,7 +3,7 @@

 preMyLibs += ../../lib/$(MACHTYPE)/jkhgap.a

 include $(kentSrc)/inc/userApp.mk

 HG_INC += -I../../hg/inc

-L += $(MYSQLLIBS) -lm

+L += $(MYSQLLIBS) -lm -lz

 

 test::

 	cd tests && ${MAKE} test



--- ./src/utils/bigWigCorrelate/makefile.orig	2023-03-27 14:36:23.117545553 +0000

+++ ./src/utils/bigWigCorrelate/makefile	2023-03-27 14:36:33.854328176 +0000

@@ -1,3 +1,4 @@

 kentSrc = ../..

 A = bigWigCorrelate

 include $(kentSrc)/inc/userApp.mk

+L += -lz

pkgs/development/perl-modules/Bio-BigFile/default.nix

0 → 100644
+66 −0
Original line number Diff line number Diff line 
{

 BioPerl,

 IOString,

 buildPerlModule,

 fetchFromGitHub,

 fetchpatch,

 fetchurl,

 kent,

 lib,

 libmysqlclient,

 libpng,

 openssl,

 perl

}:



buildPerlModule rec {

  pname = "Bio-BigFile";

  version = "1.07";



  src = fetchurl {

    url = "mirror://cpan/authors/id/L/LD/LDS/Bio-BigFile-${version}.tar.gz";

    sha256 = "277b66ce8acbdd52399e2c5a0cf4e3bd5c74c12b94877cd383d0c4c97740d16d";

  };



  # Only kent 335 works with Bio-BigFile, see

  # - official documentation: https://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#bigfile

  # - one of the developer's answer: https://github.com/Ensembl/ensembl-vep/issues/1412

  # KENT_SRC is needed for building BioBigfil

  KENT_SRC = kent.overrideAttrs (old: rec {

    pname = "kent";

    version = "335";



    src = fetchFromGitHub {

      owner = "ucscGenomeBrowser";

      repo = "kent";

      rev = "v${version}_base";

      sha256 = "1455dwzpaq4hyhcqj3fpwgq5a39kp46qarfbr6ms6l2lz583r083";

    };



    # The first patch is a custom fix  for linking error with zlib.

    patches = [

      ./kent-utils.patch

      (fetchpatch {

        url = "https://github.com/ucscGenomeBrowser/kent/commit/316e4fd40f53c96850128fd65097a42623d1e736.patch";

        sha256 = "sha256-wr3NP5qoSonKz1TLKtQyrTPErCOk2gC1RimcX0tE7cM=";

      })];

  });





  buildInputs = [

    BioPerl

    IOString

    libpng

    libmysqlclient

    openssl

  ];



  hardeningDisable = [ "format" ];



  meta = with lib; {

    homepage = "https://metacpan.org/dist/Bio-BigFile";

    description = "Manipulate Jim Kent's BigWig and BigBed index files for genomic features";

    license = licenses.unfree;

    maintainers = with maintainers; [ apraga ];

  };

}

pkgs/development/perl-modules/Bio-BigFile/kent-utils.patch

0 → 100644
+27 −0
Original line number Diff line number Diff line 
--- ./src/utils/bigWigCat/makefile	2023-03-27 14:03:01.585896516 +0000

+++ ./src/utils/bigWigCat/makefile	2023-03-27 14:03:27.716180479 +0000

@@ -1,3 +1,4 @@

 kentSrc = ../..

 A = bigWigCat

 include $(kentSrc)/inc/userApp.mk

+L += -lz



--- ./src/utils/pslLiftSubrangeBlat/makefile	1970-01-01 00:00:01.000000000 +0000

+++ ./src/utils/pslLiftSubrangeBlat/makefile	2023-03-27 14:36:59.044600213 +0000

@@ -3,7 +3,7 @@

 preMyLibs += ../../lib/$(MACHTYPE)/jkhgap.a

 include $(kentSrc)/inc/userApp.mk

 HG_INC += -I../../hg/inc

-L += $(MYSQLLIBS) -lm

+L += $(MYSQLLIBS) -lm -lz

 

 test::

 	cd tests && ${MAKE} test



--- ./src/utils/bigWigCorrelate/makefile	2023-03-27 14:36:23.117545553 +0000

+++ ./src/utils/bigWigCorrelate/makefile	2023-03-27 14:36:33.854328176 +0000

@@ -1,3 +1,4 @@

 kentSrc = ../..

 A = bigWigCorrelate

 include $(kentSrc)/inc/userApp.mk

+L += -lz

pkgs/top-level/perl-packages.nix

+2 −0
Original line number Diff line number Diff line
@@ -1761,6 +1761,8 @@ with self; { 
    };

  };













  BioBigFile = callPackage ../development/perl-modules/Bio-BigFile { };



























  BioPerl = buildPerlPackage {















    pname = "BioPerl";















    version = "1.7.8";