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Merge pull request #25594 from mimadrid/update/htslib-1.4

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Update/htslib 1.4
This commit is contained in:
Jörg Thalheim 2017-05-11 07:08:56 +01:00 committed by GitHub
commit be19ad150c
3 changed files with 21 additions and 14 deletions
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11
pkgs/applications/science/biology/bcftools/default.nix
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@ -1,16 +1,17 @@
{ stdenv, fetchurl, zlib, htslib }: { stdenv, fetchurl, htslib, zlib, bzip2, lzma, perl }:
stdenv.mkDerivation rec { stdenv.mkDerivation rec {
name = "${pname}-${version}"; name = "${pname}-${version}";
pname = "bcftools"; pname = "bcftools";
version = "1.3.1"; major = "1.4";
version = "${major}.0";
src = fetchurl { src = fetchurl {
url = "https://github.com/samtools/${pname}/releases/download/${version}/${name}.tar.bz2"; url = "https://github.com/samtools/bcftools/releases/download/${major}/bcftools-${major}.tar.bz2";
sha256 = "095ry68vmz9q5s1scjsa698dhgyvgw5aicz24c19iwfbai07mhqj"; sha256 = "0k93mq3lf73dch81p4zxi0bdll567acxfa81qzbzkqflgsjb1ccg";
}; };
buildInputs = [ zlib ]; buildInputs = [ zlib bzip2 lzma perl ];
makeFlags = [ makeFlags = [
"HSTDIR=${htslib}" "HSTDIR=${htslib}"

9
pkgs/applications/science/biology/samtools/default.nix
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@ -3,14 +3,15 @@
stdenv.mkDerivation rec { stdenv.mkDerivation rec {
name = "${pname}-${version}"; name = "${pname}-${version}";
pname = "samtools"; pname = "samtools";
version = "1.3.1"; major = "1.4";
version = "${major}.0";
src = fetchurl { src = fetchurl {
url = "https://github.com/samtools/${pname}/releases/download/${version}/${name}.tar.bz2"; url = "https://github.com/samtools/samtools/releases/download/${major}/samtools-${major}.tar.bz2";
sha256 = "0znnnxc467jbf1as2dpskrjhfh8mbll760j6w6rdkwlwbqsp8gbc"; sha256 = "1x73c0lxvd58ghrmaqqyp56z7bkmp28a71fk4ap82j976pw5pbls";
}; };
buildInputs = [ zlib ncurses htslib ]; buildInputs = [ zlib ncurses ];
configureFlags = [ "--with-htslib=${htslib}" ] configureFlags = [ "--with-htslib=${htslib}" ]
++ stdenv.lib.optional (ncurses == null) "--without-curses"; ++ stdenv.lib.optional (ncurses == null) "--without-curses";

15
pkgs/development/libraries/science/biology/htslib/default.nix
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@ -1,16 +1,21 @@
{ stdenv, fetchurl, zlib }: { stdenv, fetchurl, zlib, bzip2, lzma, curl }:
stdenv.mkDerivation rec { stdenv.mkDerivation rec {
name = "${pname}-${version}"; name = "${pname}-${version}";
version = "${major}.0";
pname = "htslib"; pname = "htslib";
version = "1.3.2"; major = "1.4";
src = fetchurl { src = fetchurl {
url = "https://github.com/samtools/${pname}/releases/download/${version}/${name}.tar.bz2"; url = "https://github.com/samtools/htslib/releases/download/${major}/htslib-${major}.tar.bz2";
sha256 = "0iq3blw23s55vkr1z88p9y2dqrb2dybzhl6hz2nlk53ncihrxcdr"; sha256 = "0l1ki3sqfhawfn7fx9v7i2pm725jki4c5zij9j96xka5zwc8iz2w";
}; };
buildInputs = [ zlib ]; buildInputs = [ zlib bzip2 lzma curl ];
configureFlags = "--enable-libcurl"; # optional but strongly recommended
installFlags = "prefix=$(out)";
meta = with stdenv.lib; { meta = with stdenv.lib; {
description = "A C library for reading/writing high-throughput sequencing data"; description = "A C library for reading/writing high-throughput sequencing data";