Merge pull request #29963 from mimadrid/update/samtools-1.6.0
samtools: 1.5.0 -> 1.6.0
This commit is contained in:
commit
047c576353
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@ -1,17 +1,18 @@
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{ stdenv, fetchurl, htslib, zlib, bzip2, lzma, perl }:
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{ stdenv, fetchurl, htslib, zlib, bzip2, lzma, curl, perl, bash }:
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stdenv.mkDerivation rec {
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name = "${pname}-${version}";
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pname = "bcftools";
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major = "1.5";
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version = "${major}.0";
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version = "1.6";
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src = fetchurl {
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url = "https://github.com/samtools/bcftools/releases/download/${major}/bcftools-${major}.tar.bz2";
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sha256 = "0093hkkvxmbwfaa7905s6185jymynvg42kq6sxv7fili11l5mxwz";
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url = "https://github.com/samtools/bcftools/releases/download/${version}/${name}.tar.bz2";
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sha256 = "10prgmf09a13mk18840938ijqgfc9y92hfc7sa2gcv07ddri0c19";
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};
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buildInputs = [ zlib bzip2 lzma perl ];
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nativeBuildInputs = [ perl ];
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buildInputs = [ htslib zlib bzip2 lzma curl ];
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makeFlags = [
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"HSTDIR=${htslib}"
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@ -19,6 +20,16 @@ stdenv.mkDerivation rec {
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"CC=cc"
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];
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preCheck = ''
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patchShebangs misc/
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patchShebangs test/
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sed -ie 's|/bin/bash|${bash}/bin/bash|' test/test.pl
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'';
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enableParallelBuilding = true;
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doCheck = true;
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meta = with stdenv.lib; {
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description = "Tools for manipulating BCF2/VCF/gVCF format, SNP and short indel sequence variants";
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license = licenses.mit;
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@ -1,21 +1,30 @@
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{ stdenv, fetchurl, zlib, htslib, ncurses ? null }:
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{ stdenv, fetchurl, zlib, htslib, perl, ncurses ? null }:
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stdenv.mkDerivation rec {
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name = "${pname}-${version}";
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pname = "samtools";
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major = "1.5";
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version = "${major}.0";
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version = "1.6";
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src = fetchurl {
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url = "https://github.com/samtools/samtools/releases/download/${major}/samtools-${major}.tar.bz2";
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sha256 = "1xidmv0jmfy7l0kb32hdnlshcxgzi1hmygvig0cqrq1fhckdlhl5";
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url = "https://github.com/samtools/samtools/releases/download/${version}/${name}.tar.bz2";
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sha256 = "17p4vdj2j2qr3b2c0v4100h6cg4jj3zrb4dmdnd9d9aqs74d4p7f";
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};
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buildInputs = [ zlib ncurses ];
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nativeBuildInputs = [ perl ];
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buildInputs = [ zlib ncurses htslib ];
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configureFlags = [ "--with-htslib=${htslib}" ]
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++ stdenv.lib.optional (ncurses == null) "--without-curses";
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preCheck = ''
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patchShebangs test/
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'';
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enableParallelBuilding = true;
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doCheck = true;
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meta = with stdenv.lib; {
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description = "Tools for manipulating SAM/BAM/CRAM format";
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license = licenses.mit;
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@ -1,22 +1,32 @@
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{ stdenv, fetchurl, zlib, bzip2, lzma, curl }:
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{ stdenv, fetchurl, zlib, bzip2, lzma, curl, perl }:
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stdenv.mkDerivation rec {
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name = "${pname}-${version}";
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version = "${major}.0";
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pname = "htslib";
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major = "1.5";
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version = "1.6";
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src = fetchurl {
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url = "https://github.com/samtools/htslib/releases/download/${major}/htslib-${major}.tar.bz2";
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sha256 = "0bcjmnbwp2bib1z1bkrp95w9v2syzdwdfqww10mkb1hxlmg52ax0";
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url = "https://github.com/samtools/htslib/releases/download/${version}/${name}.tar.bz2";
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sha256 = "1jsca3hg4rbr6iqq6imkj4lsvgl8g9768bcmny3hlff2w25vx24m";
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};
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# perl is only used during the check phase.
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nativeBuildInputs = [ perl ];
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buildInputs = [ zlib bzip2 lzma curl ];
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configureFlags = "--enable-libcurl"; # optional but strongly recommended
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installFlags = "prefix=$(out)";
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preCheck = ''
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patchShebangs test/
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'';
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enableParallelBuilding = true;
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doCheck = true;
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meta = with stdenv.lib; {
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description = "A C library for reading/writing high-throughput sequencing data";
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license = licenses.mit;
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@ -25,4 +35,3 @@ stdenv.mkDerivation rec {
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maintainers = [ maintainers.mimadrid ];
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};
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}
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