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
- e027a5d8368a053e231 : packaging kent header
- 2b2c6f4c287c6107acb : enabling patches in kent

2 files changed, 93 insertions, 0 deletions

diff --git a/pkgs/development/perl-modules/Bio-BigFile/default.nix b/pkgs/development/perl-modules/Bio-BigFile/default.nix
new file mode 100644
index 0000000000000..a84b218239783
--- /dev/null
+++ b/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-${version}.tar.gz";
+    sha256 = "277b66ce8acbdd52399e2c5a0cf4e3bd5c74c12b94877cd383d0c4c97740d16d";
+  };
+
+  # Only kent 335 works with Bio-BigFile, see
+  # - official documentation: https://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#bigfile
+  # - one of the developer's answer: https://github.com/Ensembl/ensembl-vep/issues/1412
+  # KENT_SRC is needed for building BioBigfil
+  KENT_SRC = kent.overrideAttrs (old: rec {
+    pname = "kent";
+    version = "335";
+
+    src = fetchFromGitHub {
+      owner = "ucscGenomeBrowser";
+      repo = "kent";
+      rev = "v${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 ];
+  };
+}
diff --git a/pkgs/development/perl-modules/Bio-BigFile/kent-utils.patch b/pkgs/development/perl-modules/Bio-BigFile/kent-utils.patch
new file mode 100644
index 0000000000000..0c1db4d6c66ca
--- /dev/null
+++ b/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