Merge pull request #186462 from apraga/bio-bigfile-1.07

  buildInputs = [ libpng libuuid zlib bzip2 xz openssl curl libmysqlclient ];

  patchPhase = ''

    runHook prePatch

  postPatch = ''

    substituteInPlace ./src/checkUmask.sh \

      --replace "/bin/bash" "${bash}/bin/bash"

    substituteInPlace ./src/hg/sqlEnvTest.sh \

      --replace "which mysql_config" "${which}/bin/which ${libmysqlclient}/bin/mysql_config"

    runHook postPatch

  '';

  buildPhase = ''

{

 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

  # BioBigfile needs the environment variable KENT_SRC to find kent

  KENT_SRC = kent.overrideAttrs (old: rec {

    pname = "kent";

    version = "335";

    src = fetchFromGitHub {

      owner = "ucscGenomeBrowser";

      repo = "kent";

      rev = "v${version}_base";

      sha256 = "1455dwzpaq4hyhcqj3fpwgq5a39kp46qarfbr6ms6l2lz583r083";

    };

    patches = [

      # Fix  for linking error with zlib. Adding zlib as a dependency is not enough

      ./kent-utils.patch

      # Vendoring upstream patch (not merged in uscsGenomeBrowser/kent)

      ./kent-316e4fd40f53c96850128fd65097a42623d1e736.patch

    ];

  });

  buildInputs = [

    BioPerl

    IOString

    libpng

    libmysqlclient

    openssl

  ];

  # Ensure compatibility with GCC-11 (compilation fails if -Wno-format-security)

  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.artistic2;

    maintainers = with maintainers; [ apraga ];

  };

}

From 316e4fd40f53c96850128fd65097a42623d1e736 Mon Sep 17 00:00:00 2001

From: Marcel Bargull <marcel.bargull@udo.edu>

Date: Sat, 27 Mar 2021 16:23:34 +0100

Subject: [PATCH] Fix linking Clang 11 compiled objects

With Clang 11 htmlRecover from lib/htmshell.h is picked up as a

definition, not just declaration of the jmp_buf. As such both

lib/htmshell.c and hg/lib/cart.c export two symbols with the same name.

---

 src/inc/htmshell.h | 2 +-

 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/inc/htmshell.h b/src/inc/htmshell.h

index 9d85f45b936..dd586db761c 100644

--- a/src/inc/htmshell.h

+++ b/src/inc/htmshell.h

@@ -160,7 +160,7 @@ void htmlBadVar(char *varName);

 void htmlImage(char *fileName, int width, int height);

 /* Display centered image file. */

-jmp_buf htmlRecover;  /* Error recovery jump. Exposed for cart's use. */

+extern jmp_buf htmlRecover;  /* Error recovery jump. Exposed for cart's use. */

 void htmlVaWarn(char *format, va_list args);

 /* Write an error message.  (Generally you just call warn() or errAbort().

--- ./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

    };

  };

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

  BioPerl = buildPerlPackage {

    pname = "BioPerl";

    version = "1.7.8";