commit cc4bd303877c3eb2db186ca214712f54dbe69bae · pyrox.dev/nixpkgs

+27

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

···

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       --- ./src/utils/bigWigCat/makefile.orig	2023-03-27 14:03:01.585896516 +0000

     

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

     

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

     

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        kentSrc = ../..

     

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        A = bigWigCat

     

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        include $(kentSrc)/inc/userApp.mk

     

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       +L += -lz

     

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       +
       

     

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

     

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

     

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

     

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

     

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        include $(kentSrc)/inc/userApp.mk

     

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

     

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       -L += $(MYSQLLIBS) -lm

     

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

     

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       +
        

     

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        test::

     

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        	cd tests && ${MAKE} test

     

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

     

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

     

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

     

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        kentSrc = ../..

     

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        A = bigWigCorrelate

     

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        include $(kentSrc)/inc/userApp.mk

     

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       +L += -lz

+66

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

···

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       {

     

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        BioPerl,

     

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        IOString,

     

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        buildPerlModule,

     

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        fetchFromGitHub,

     

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        fetchpatch,

     

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        fetchurl,

     

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        kent,

     

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        lib,

     

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        libmysqlclient,

     

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        libpng,

     

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        openssl,

     

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        perl

     

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       }:

     

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       buildPerlModule rec {

     

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         pname = "Bio-BigFile";

     

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         version = "1.07";

     

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         src = fetchurl {

     

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

     

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           sha256 = "277b66ce8acbdd52399e2c5a0cf4e3bd5c74c12b94877cd383d0c4c97740d16d";

     

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         };

     

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         # Only kent 335 works with Bio-BigFile, see

     

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

     

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

     

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         # KENT_SRC is needed for building BioBigfil

     

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         KENT_SRC = kent.overrideAttrs (old: rec {

     

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           pname = "kent";

     

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           version = "335";

     

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           src = fetchFromGitHub {

     

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             owner = "ucscGenomeBrowser";

     

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             repo = "kent";

     

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             rev = "v${version}_base";

     

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             sha256 = "1455dwzpaq4hyhcqj3fpwgq5a39kp46qarfbr6ms6l2lz583r083";

     

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           };

     

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

     

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           patches = [

     

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             ./kent-utils.patch

     

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             (fetchpatch {

     

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

     

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               sha256 = "sha256-wr3NP5qoSonKz1TLKtQyrTPErCOk2gC1RimcX0tE7cM=";

     

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             })];

     

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         });

     

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         buildInputs = [

     

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           BioPerl

     

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           IOString

     

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           libpng

     

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           libmysqlclient

     

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           openssl

     

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         ];

     

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         hardeningDisable = [ "format" ];

     

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         meta = with lib; {

     

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

     

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

     

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           license = licenses.unfree;

     

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           maintainers = with maintainers; [ apraga ];

     

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         };

     

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       }

+27

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

···

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       --- ./src/utils/bigWigCat/makefile	2023-03-27 14:03:01.585896516 +0000

     

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

     

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

     

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        kentSrc = ../..

     

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        A = bigWigCat

     

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        include $(kentSrc)/inc/userApp.mk

     

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       +L += -lz

     

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

     

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

     

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

     

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

     

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        include $(kentSrc)/inc/userApp.mk

     

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

     

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       -L += $(MYSQLLIBS) -lm

     

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

     

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        test::

     

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        	cd tests && ${MAKE} test

     

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

     

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

     

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

     

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        kentSrc = ../..

     

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        A = bigWigCorrelate

     

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        include $(kentSrc)/inc/userApp.mk

     

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       +L += -lz

pkgs/top-level/perl-packages.nix

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           };

     

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         };

     

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

     

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         BioPerl = buildPerlPackage {

     

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           pname = "BioPerl";

     

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           version = "1.7.8";