diff options
Diffstat (limited to 'pkgs/applications/science/biology')
-rw-r--r-- | pkgs/applications/science/biology/bcftools/default.nix | 26 | ||||
-rw-r--r-- | pkgs/applications/science/biology/samtools/default.nix | 16 |
2 files changed, 37 insertions, 5 deletions
diff --git a/pkgs/applications/science/biology/bcftools/default.nix b/pkgs/applications/science/biology/bcftools/default.nix new file mode 100644 index 000000000000..d4e4ed5b954f --- /dev/null +++ b/pkgs/applications/science/biology/bcftools/default.nix @@ -0,0 +1,26 @@ +{ stdenv, fetchurl, zlib, htslib }: + +stdenv.mkDerivation rec { + name = "${pname}-${version}"; + pname = "bcftools"; + version = "1.3.1"; + + src = fetchurl { + url = "https://github.com/samtools/${pname}/releases/download/${version}/${name}.tar.bz2"; + sha256 = "095ry68vmz9q5s1scjsa698dhgyvgw5aicz24c19iwfbai07mhqj"; + }; + + buildInputs = [ zlib ]; + + preBuild = '' + makeFlagsArray=("HSTDIR=${htslib}" "prefix=$out") + ''; + + meta = with stdenv.lib; { + description = "Tools for manipulating BCF2/VCF/gVCF format, SNP and short indel sequence variants"; + license = licenses.mit; + homepage = http://www.htslib.org/; + platforms = platforms.unix; + maintainers = [ maintainers.mimadrid ]; + }; +} diff --git a/pkgs/applications/science/biology/samtools/default.nix b/pkgs/applications/science/biology/samtools/default.nix index 9535609fa783..e97af1ea0ee6 100644 --- a/pkgs/applications/science/biology/samtools/default.nix +++ b/pkgs/applications/science/biology/samtools/default.nix @@ -1,19 +1,25 @@ -{ stdenv, fetchurl, zlib, ncurses }: +{ stdenv, fetchurl, zlib, htslib, ncurses ? null }: stdenv.mkDerivation rec { - name = "samtools-${version}"; + name = "${pname}-${version}"; + pname = "samtools"; version = "1.3.1"; src = fetchurl { - url = "https://github.com/samtools/samtools/releases/download/${version}/${name}.tar.bz2"; + url = "https://github.com/samtools/${pname}/releases/download/${version}/${name}.tar.bz2"; sha256 = "0znnnxc467jbf1as2dpskrjhfh8mbll760j6w6rdkwlwbqsp8gbc"; }; - buildInputs = [ zlib ncurses ]; + buildInputs = [ zlib ncurses htslib ]; + + configureFlags = [ "--with-htslib=${htslib}" ] + ++ stdenv.lib.optional (ncurses == null) "--without-curses"; meta = with stdenv.lib; { - description = "Tools (written in C using htslib) for manipulating next-generation sequencing data"; + description = "Tools for manipulating SAM/BAM/CRAM format"; license = licenses.mit; homepage = http://www.htslib.org/; + platforms = platforms.unix; + maintainers = [ maintainers.mimadrid ]; }; } |