Merge pull request #16379 from mimadrid/init/bcftools-1.3.1

bcftools: init at 1.3.1

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 ];
   };
 }