Merge pull request #34530 from unode/samtools-old

samtools-old: init at 0.1.19

pkgs/applications/science/biology/samtools/samtools-0.1.19-no-curses.patch

@@ -0,0 +1,22 @@
+diff --git a/Makefile b/Makefile
+index 2f51bfc..395d6f1 100644
+--- a/Makefile
++++ b/Makefile
+@@ -1,7 +1,7 @@
+ CC=			gcc
+ CFLAGS=		-g -Wall -O2
+ #LDFLAGS=		-Wl,-rpath,\$$ORIGIN/../lib
+-DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
++DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE # -D_CURSES_LIB=1
+ KNETFILE_O=	knetfile.o
+ LOBJS=		bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o	\
+ 			bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \
+@@ -15,7 +15,7 @@ PROG=		samtools
+ INCLUDES=	-I.
+ SUBDIRS=	. bcftools misc
+ LIBPATH=
+-LIBCURSES=	-lcurses # -lXCurses
++LIBCURSES=	# -lcurses # -lXCurses
+ 
+ .SUFFIXES:.c .o
+ .PHONY: all lib

pkgs/applications/science/biology/samtools/samtools_0_1_19.nix

@@ -0,0 +1,34 @@
+{ stdenv, fetchurl, zlib }:
+
+stdenv.mkDerivation rec {
+  name = "${pname}-${version}";
+  pname = "samtools";
+  version = "0.1.19";
+
+  src = fetchurl {
+    url = "mirror://sourceforge/samtools/${name}.tar.bz2";
+    sha256 = "d080c9d356e5f0ad334007e4461cbcee3c4ca97b8a7a5a48c44883cf9dee63d4";
+  };
+
+  patches = [
+    ./samtools-0.1.19-no-curses.patch
+  ];
+
+  buildInputs = [ zlib ];
+
+  installPhase = ''
+    mkdir -p $out/bin
+    mkdir -p $out/share/man
+
+    cp samtools $out/bin
+    cp samtools.1 $out/share/man
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Tools for manipulating SAM/BAM/CRAM format";
+    license = licenses.mit;
+    homepage = http://samtools.sourceforge.net/;
+    platforms = platforms.unix;
+    maintainers = [ maintainers.unode ];
+  };
+}

pkgs/top-level/all-packages.nix

@@ -19117,6 +19117,7 @@ with pkgs;
   });
 
   samtools = callPackage ../applications/science/biology/samtools/default.nix { };
+  samtools_0_1_19 = callPackage ../applications/science/biology/samtools/samtools_0_1_19.nix { };
 
   snpeff = callPackage ../applications/science/biology/snpeff/default.nix { };