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

bio-bigfile: init 1.07

pkgs/applications/science/biology/kent/default.nix

@@ -24,16 +24,12 @@ stdenv.mkDerivation rec {
 
   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 = ''

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

@@ -0,0 +1,66 @@
+{
+ 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 ];
+  };
+}

pkgs/development/perl-modules/Bio-BigFile/kent-316e4fd40f53c96850128fd65097a42623d1e736.patch

@@ -0,0 +1,25 @@
+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().

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

@@ -0,0 +1,27 @@
+--- ./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

@@ -1803,6 +1803,8 @@ with self; {
     };
   };
 
+  BioBigFile = callPackage ../development/perl-modules/Bio-BigFile { };
+
   BioPerl = buildPerlPackage {
     pname = "BioPerl";
     version = "1.7.8";