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Merge pull request #34530 from unode/samtools-old

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samtools-old: init at 0.1.19
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Jörg Thalheim 2018-02-10 08:34:26 +00:00 committed by GitHub
parent d8d8a0a00f 65ea5f8857
commit 08d1400816
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22
pkgs/applications/science/biology/samtools/samtools-0.1.19-no-curses.patch Normal file
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@ -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

34
pkgs/applications/science/biology/samtools/samtools_0_1_19.nix Normal file
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@ -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 ];
};
}

1
pkgs/top-level/all-packages.nix
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@ -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 { };