From 25b17ae1d78e0c2d48ac4a16a70f548661570add Mon Sep 17 00:00:00 2001 From: mimadrid Date: Sat, 30 Sep 2017 19:43:19 +0200 Subject: [PATCH 1/6] htslib: 1.5.0 -> 1.6.0 --- .../libraries/science/biology/htslib/default.nix | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/pkgs/development/libraries/science/biology/htslib/default.nix b/pkgs/development/libraries/science/biology/htslib/default.nix index 5a08e32e7e9..a7e1c46c70a 100644 --- a/pkgs/development/libraries/science/biology/htslib/default.nix +++ b/pkgs/development/libraries/science/biology/htslib/default.nix @@ -1,22 +1,32 @@ -{ stdenv, fetchurl, zlib, bzip2, lzma, curl }: +{ stdenv, fetchurl, zlib, bzip2, lzma, curl, perl }: stdenv.mkDerivation rec { name = "${pname}-${version}"; version = "${major}.0"; pname = "htslib"; - major = "1.5"; + major = "1.6"; src = fetchurl { url = "https://github.com/samtools/htslib/releases/download/${major}/htslib-${major}.tar.bz2"; - sha256 = "0bcjmnbwp2bib1z1bkrp95w9v2syzdwdfqww10mkb1hxlmg52ax0"; + sha256 = "1jsca3hg4rbr6iqq6imkj4lsvgl8g9768bcmny3hlff2w25vx24m"; }; + propagatedNativeBuildInputs = [ perl ]; + buildInputs = [ zlib bzip2 lzma curl ]; configureFlags = "--enable-libcurl"; # optional but strongly recommended installFlags = "prefix=$(out)"; + enableParallelBuilding = true; + + doCheck = true; + + preCheck = '' + find test -name "*.pl" -exec sed -ie 's|/usr/bin/\(env[[:space:]]\)\{0,1\}perl|${perl}/bin/perl|' {} + + ''; + meta = with stdenv.lib; { description = "A C library for reading/writing high-throughput sequencing data"; license = licenses.mit; From ee2c76693e0ac2917fc74c737e0eee18a852fe6c Mon Sep 17 00:00:00 2001 From: mimadrid Date: Sat, 30 Sep 2017 19:44:48 +0200 Subject: [PATCH 2/6] samtools: 1.5.0 -> 1.6.0 --- .../science/biology/samtools/default.nix | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/pkgs/applications/science/biology/samtools/default.nix b/pkgs/applications/science/biology/samtools/default.nix index f8391a2d6b3..0f1f4692eb7 100644 --- a/pkgs/applications/science/biology/samtools/default.nix +++ b/pkgs/applications/science/biology/samtools/default.nix @@ -1,21 +1,31 @@ -{ stdenv, fetchurl, zlib, htslib, ncurses ? null }: +{ stdenv, fetchurl, zlib, htslib, perl, ncurses ? null }: stdenv.mkDerivation rec { name = "${pname}-${version}"; pname = "samtools"; - major = "1.5"; + major = "1.6"; version = "${major}.0"; src = fetchurl { url = "https://github.com/samtools/samtools/releases/download/${major}/samtools-${major}.tar.bz2"; - sha256 = "1xidmv0jmfy7l0kb32hdnlshcxgzi1hmygvig0cqrq1fhckdlhl5"; + sha256 = "17p4vdj2j2qr3b2c0v4100h6cg4jj3zrb4dmdnd9d9aqs74d4p7f"; }; buildInputs = [ zlib ncurses ]; + propagatedBuildInputs = [ htslib ]; + configureFlags = [ "--with-htslib=${htslib}" ] ++ stdenv.lib.optional (ncurses == null) "--without-curses"; + enableParallelBuilding = true; + + doCheck = true; + + preCheck = '' + sed -ie 's|/usr/bin/\(env[[:space:]]\)\{0,1\}perl|${perl}/bin/perl|' test/test.pl + ''; + meta = with stdenv.lib; { description = "Tools for manipulating SAM/BAM/CRAM format"; license = licenses.mit; From bebccf176effdb520f5c1ee0087caf6d10b9cd54 Mon Sep 17 00:00:00 2001 From: mimadrid Date: Sat, 30 Sep 2017 19:45:26 +0200 Subject: [PATCH 3/6] bcftools: 1.5.0 -> 1.6.0 --- .../science/biology/bcftools/default.nix | 22 +++++++++++++++---- 1 file changed, 18 insertions(+), 4 deletions(-) diff --git a/pkgs/applications/science/biology/bcftools/default.nix b/pkgs/applications/science/biology/bcftools/default.nix index cfd72601d1e..b6fc8af4324 100644 --- a/pkgs/applications/science/biology/bcftools/default.nix +++ b/pkgs/applications/science/biology/bcftools/default.nix @@ -1,17 +1,22 @@ -{ stdenv, fetchurl, htslib, zlib, bzip2, lzma, perl }: +{ stdenv, fetchurl, htslib, zlib, bzip2, lzma, perl, bash }: stdenv.mkDerivation rec { name = "${pname}-${version}"; pname = "bcftools"; - major = "1.5"; + major = "1.6"; version = "${major}.0"; src = fetchurl { url = "https://github.com/samtools/bcftools/releases/download/${major}/bcftools-${major}.tar.bz2"; - sha256 = "0093hkkvxmbwfaa7905s6185jymynvg42kq6sxv7fili11l5mxwz"; + sha256 = "10prgmf09a13mk18840938ijqgfc9y92hfc7sa2gcv07ddri0c19"; }; - buildInputs = [ zlib bzip2 lzma perl ]; + + nativeBuildInputs = [ bash ]; + + buildInputs = [ zlib bzip2 lzma ]; + + propagatedBuildInputs = [ htslib ]; makeFlags = [ "HSTDIR=${htslib}" @@ -19,6 +24,15 @@ stdenv.mkDerivation rec { "CC=cc" ]; + enableParallelBuilding = true; + + doCheck = true; + + preCheck = '' + sed -ie 's|/usr/bin/\(env[[:space:]]\)\{0,1\}perl|${perl}/bin/perl|' test/test.pl test/csq/{sort-csq,make-csq-test} misc/plot-vcfstats + sed -ie 's|/bin/bash|${bash}/bin/bash|' test/test.pl + ''; + meta = with stdenv.lib; { description = "Tools for manipulating BCF2/VCF/gVCF format, SNP and short indel sequence variants"; license = licenses.mit; From 0acf94bb9fa466d106e8e63884304d5ccdb37a6e Mon Sep 17 00:00:00 2001 From: Orivej Desh Date: Sun, 1 Oct 2017 07:12:52 +0000 Subject: [PATCH 4/6] htslib: fix up --- .../science/biology/htslib/default.nix | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/pkgs/development/libraries/science/biology/htslib/default.nix b/pkgs/development/libraries/science/biology/htslib/default.nix index a7e1c46c70a..b3c6d9f26d4 100644 --- a/pkgs/development/libraries/science/biology/htslib/default.nix +++ b/pkgs/development/libraries/science/biology/htslib/default.nix @@ -2,16 +2,16 @@ stdenv.mkDerivation rec { name = "${pname}-${version}"; - version = "${major}.0"; pname = "htslib"; - major = "1.6"; + version = "1.6"; src = fetchurl { - url = "https://github.com/samtools/htslib/releases/download/${major}/htslib-${major}.tar.bz2"; + url = "https://github.com/samtools/htslib/releases/download/${version}/${name}.tar.bz2"; sha256 = "1jsca3hg4rbr6iqq6imkj4lsvgl8g9768bcmny3hlff2w25vx24m"; }; - propagatedNativeBuildInputs = [ perl ]; + # perl is only used during the check phase. + nativeBuildInputs = [ perl ]; buildInputs = [ zlib bzip2 lzma curl ]; @@ -19,14 +19,14 @@ stdenv.mkDerivation rec { installFlags = "prefix=$(out)"; + preCheck = '' + patchShebangs test/ + ''; + enableParallelBuilding = true; doCheck = true; - preCheck = '' - find test -name "*.pl" -exec sed -ie 's|/usr/bin/\(env[[:space:]]\)\{0,1\}perl|${perl}/bin/perl|' {} + - ''; - meta = with stdenv.lib; { description = "A C library for reading/writing high-throughput sequencing data"; license = licenses.mit; @@ -35,4 +35,3 @@ stdenv.mkDerivation rec { maintainers = [ maintainers.mimadrid ]; }; } - From 09a53969828ead5dd6a231e5db3b4a765fca47d3 Mon Sep 17 00:00:00 2001 From: Orivej Desh Date: Sun, 1 Oct 2017 07:30:56 +0000 Subject: [PATCH 5/6] samtools: fix up --- .../science/biology/samtools/default.nix | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/pkgs/applications/science/biology/samtools/default.nix b/pkgs/applications/science/biology/samtools/default.nix index 0f1f4692eb7..640f32671bb 100644 --- a/pkgs/applications/science/biology/samtools/default.nix +++ b/pkgs/applications/science/biology/samtools/default.nix @@ -3,29 +3,28 @@ stdenv.mkDerivation rec { name = "${pname}-${version}"; pname = "samtools"; - major = "1.6"; - version = "${major}.0"; + version = "1.6"; src = fetchurl { - url = "https://github.com/samtools/samtools/releases/download/${major}/samtools-${major}.tar.bz2"; + url = "https://github.com/samtools/samtools/releases/download/${version}/${name}.tar.bz2"; sha256 = "17p4vdj2j2qr3b2c0v4100h6cg4jj3zrb4dmdnd9d9aqs74d4p7f"; }; - buildInputs = [ zlib ncurses ]; + nativeBuildInputs = [ perl ]; - propagatedBuildInputs = [ htslib ]; + buildInputs = [ zlib ncurses htslib ]; configureFlags = [ "--with-htslib=${htslib}" ] ++ stdenv.lib.optional (ncurses == null) "--without-curses"; + preCheck = '' + patchShebangs test/ + ''; + enableParallelBuilding = true; doCheck = true; - preCheck = '' - sed -ie 's|/usr/bin/\(env[[:space:]]\)\{0,1\}perl|${perl}/bin/perl|' test/test.pl - ''; - meta = with stdenv.lib; { description = "Tools for manipulating SAM/BAM/CRAM format"; license = licenses.mit; From d73bd7f50ab09ad511851f9b2ee812cc17136edf Mon Sep 17 00:00:00 2001 From: Orivej Desh Date: Sun, 1 Oct 2017 07:31:55 +0000 Subject: [PATCH 6/6] bcftools: fix up --- .../science/biology/bcftools/default.nix | 25 ++++++++----------- 1 file changed, 11 insertions(+), 14 deletions(-) diff --git a/pkgs/applications/science/biology/bcftools/default.nix b/pkgs/applications/science/biology/bcftools/default.nix index b6fc8af4324..db12fc00c87 100644 --- a/pkgs/applications/science/biology/bcftools/default.nix +++ b/pkgs/applications/science/biology/bcftools/default.nix @@ -1,22 +1,18 @@ -{ stdenv, fetchurl, htslib, zlib, bzip2, lzma, perl, bash }: +{ stdenv, fetchurl, htslib, zlib, bzip2, lzma, curl, perl, bash }: stdenv.mkDerivation rec { name = "${pname}-${version}"; pname = "bcftools"; - major = "1.6"; - version = "${major}.0"; + version = "1.6"; src = fetchurl { - url = "https://github.com/samtools/bcftools/releases/download/${major}/bcftools-${major}.tar.bz2"; + url = "https://github.com/samtools/bcftools/releases/download/${version}/${name}.tar.bz2"; sha256 = "10prgmf09a13mk18840938ijqgfc9y92hfc7sa2gcv07ddri0c19"; }; + nativeBuildInputs = [ perl ]; - nativeBuildInputs = [ bash ]; - - buildInputs = [ zlib bzip2 lzma ]; - - propagatedBuildInputs = [ htslib ]; + buildInputs = [ htslib zlib bzip2 lzma curl ]; makeFlags = [ "HSTDIR=${htslib}" @@ -24,15 +20,16 @@ stdenv.mkDerivation rec { "CC=cc" ]; + preCheck = '' + patchShebangs misc/ + patchShebangs test/ + sed -ie 's|/bin/bash|${bash}/bin/bash|' test/test.pl + ''; + enableParallelBuilding = true; doCheck = true; - preCheck = '' - sed -ie 's|/usr/bin/\(env[[:space:]]\)\{0,1\}perl|${perl}/bin/perl|' test/test.pl test/csq/{sort-csq,make-csq-test} misc/plot-vcfstats - sed -ie 's|/bin/bash|${bash}/bin/bash|' test/test.pl - ''; - meta = with stdenv.lib; { description = "Tools for manipulating BCF2/VCF/gVCF format, SNP and short indel sequence variants"; license = licenses.mit;