Merge remote-tracking branch 'origin/master' into gcc-8

36 files changed, 109 insertions, 48 deletions

diff --git a/pkgs/applications/science/biology/bcftools/default.nix b/pkgs/applications/science/biology/bcftools/default.nix
index 539d7c224463..d8ffbb74e6b0 100644
--- a/pkgs/applications/science/biology/bcftools/default.nix
+++ b/pkgs/applications/science/biology/bcftools/default.nix
@@ -1,12 +1,11 @@
 { stdenv, fetchurl, htslib, zlib, bzip2, lzma, curl, perl, python, bash }:
 
 stdenv.mkDerivation rec {
-  name = "${pname}-${version}";
   pname = "bcftools";
   version = "1.9";
 
   src = fetchurl {
-    url = "https://github.com/samtools/bcftools/releases/download/${version}/${name}.tar.bz2";
+    url = "https://github.com/samtools/bcftools/releases/download/${version}/${pname}-${version}.tar.bz2";
     sha256 = "1j3h638i8kgihzyrlnpj82xg1b23sijibys9hvwari3fy7kd0dkg";
   };
 
diff --git a/pkgs/applications/science/biology/bedtools/default.nix b/pkgs/applications/science/biology/bedtools/default.nix
index 2cdd7fda38ef..b5bc3b622b91 100644
--- a/pkgs/applications/science/biology/bedtools/default.nix
+++ b/pkgs/applications/science/biology/bedtools/default.nix
@@ -1,7 +1,7 @@
 {stdenv, fetchFromGitHub, zlib, python, bzip2, lzma}:
 
 stdenv.mkDerivation rec {
-  name = "bedtools-${version}";
+  pname = "bedtools";
   version = "2.28.0";
 
   src = fetchFromGitHub {
diff --git a/pkgs/applications/science/biology/bftools/default.nix b/pkgs/applications/science/biology/bftools/default.nix
index 24a6e052df9e..158291049347 100644
--- a/pkgs/applications/science/biology/bftools/default.nix
+++ b/pkgs/applications/science/biology/bftools/default.nix
@@ -1,7 +1,7 @@
 { stdenv, lib, makeWrapper, fetchzip, jre }:
 
 stdenv.mkDerivation rec {
-  name = "bftools-${version}";
+  pname = "bftools";
   version = "5.9.2";
 
   src = fetchzip {
diff --git a/pkgs/applications/science/biology/bowtie2/default.nix b/pkgs/applications/science/biology/bowtie2/default.nix
index 21e2f56bdf97..962428d67cf9 100644
--- a/pkgs/applications/science/biology/bowtie2/default.nix
+++ b/pkgs/applications/science/biology/bowtie2/default.nix
@@ -3,7 +3,6 @@
 stdenv.mkDerivation rec {
   pname = "bowtie2";
   version = "2.3.5.1";
-  name = "${pname}-${version}";
 
   src = fetchFromGitHub {
     owner = "BenLangmead";
diff --git a/pkgs/applications/science/biology/bwa/default.nix b/pkgs/applications/science/biology/bwa/default.nix
index d1dbacf053fb..5e39320bf835 100644
--- a/pkgs/applications/science/biology/bwa/default.nix
+++ b/pkgs/applications/science/biology/bwa/default.nix
@@ -1,11 +1,11 @@
 { stdenv, fetchurl, zlib }:
 
 stdenv.mkDerivation rec {
-  name    = "bwa-${version}";
+  pname = "bwa";
   version = "0.7.17";
 
   src = fetchurl {
-    url = "mirror://sourceforge/bio-bwa/${name}.tar.bz2";
+    url = "mirror://sourceforge/bio-bwa/${pname}-${version}.tar.bz2";
     sha256 = "1zfhv2zg9v1icdlq4p9ssc8k01mca5d1bd87w71py2swfi74s6yy";
   };
 
diff --git a/pkgs/applications/science/biology/clustal-omega/default.nix b/pkgs/applications/science/biology/clustal-omega/default.nix
index 3464e134ee85..00acc25028c0 100644
--- a/pkgs/applications/science/biology/clustal-omega/default.nix
+++ b/pkgs/applications/science/biology/clustal-omega/default.nix
@@ -2,10 +2,10 @@
 
 stdenv.mkDerivation rec {
   version = "1.2.4";
-  name = "clustal-omega-${version}";
+  pname = "clustal-omega";
 
   src = fetchurl {
-    url = "http://www.clustal.org/omega/${name}.tar.gz";
+    url = "http://www.clustal.org/omega/${pname}-${version}.tar.gz";
     sha256 = "1vm30mzncwdv881vrcwg11vzvrsmwy4wg80j5i0lcfk6dlld50w6";
   };
 
diff --git a/pkgs/applications/science/biology/dcm2niix/default.nix b/pkgs/applications/science/biology/dcm2niix/default.nix
index 0e2b5d8b25fe..63d51de9930f 100644
--- a/pkgs/applications/science/biology/dcm2niix/default.nix
+++ b/pkgs/applications/science/biology/dcm2niix/default.nix
@@ -7,7 +7,7 @@
 
 stdenv.mkDerivation rec {
   version = "1.0.20190410";
-  name = "dcm2niix-${version}";
+  pname = "dcm2niix";
 
   src = fetchFromGitHub {
     owner = "rordenlab";
diff --git a/pkgs/applications/science/biology/freebayes/default.nix b/pkgs/applications/science/biology/freebayes/default.nix
index 1a15dcf6197d..e1e84c9423bb 100644
--- a/pkgs/applications/science/biology/freebayes/default.nix
+++ b/pkgs/applications/science/biology/freebayes/default.nix
@@ -1,7 +1,7 @@
 { stdenv, fetchFromGitHub, zlib, bzip2, lzma }:
 
 stdenv.mkDerivation rec {
-  name    = "freebayes-${version}";
+  pname = "freebayes";
   version = "2017-08-23";
 
   src = fetchFromGitHub {
diff --git a/pkgs/applications/science/biology/hisat2/default.nix b/pkgs/applications/science/biology/hisat2/default.nix
index 9d41fed06911..824856301145 100644
--- a/pkgs/applications/science/biology/hisat2/default.nix
+++ b/pkgs/applications/science/biology/hisat2/default.nix
@@ -1,7 +1,7 @@
 {stdenv, fetchurl, unzip, which, python, perl}:
 
 stdenv.mkDerivation rec {
-  name = "hisat2-${version}";
+  pname = "hisat2";
   version = "2.1.0";
 
   src = fetchurl {
diff --git a/pkgs/applications/science/biology/hmmer/default.nix b/pkgs/applications/science/biology/hmmer/default.nix
index e43d48db55f3..3adbaf0079ef 100644
--- a/pkgs/applications/science/biology/hmmer/default.nix
+++ b/pkgs/applications/science/biology/hmmer/default.nix
@@ -2,10 +2,10 @@
 
 stdenv.mkDerivation rec {
   version = "3.2.1";
-  name = "hmmer-${version}";
+  pname = "hmmer";
 
   src = fetchurl {
-    url = "http://eddylab.org/software/hmmer/${name}.tar.gz";
+    url = "http://eddylab.org/software/hmmer/${pname}-${version}.tar.gz";
     sha256 = "171bivy6xhgjsz5nv53n81pc3frnwz29ylblawk2bv46szwjjqd5";
   };
 
diff --git a/pkgs/applications/science/biology/igv/default.nix b/pkgs/applications/science/biology/igv/default.nix
index 95dc2b612e22..412b55f59163 100644
--- a/pkgs/applications/science/biology/igv/default.nix
+++ b/pkgs/applications/science/biology/igv/default.nix
@@ -1,7 +1,7 @@
 { stdenv, fetchurl, unzip, jre }:
 
 stdenv.mkDerivation rec {
-  name = "igv-${version}";
+  pname = "igv";
   version = "2.4.19";
 
   src = fetchurl {
diff --git a/pkgs/applications/science/biology/itsx/default.nix b/pkgs/applications/science/biology/itsx/default.nix
index 0c8c7313bf2a..1ba8cdf22ba0 100644
--- a/pkgs/applications/science/biology/itsx/default.nix
+++ b/pkgs/applications/science/biology/itsx/default.nix
@@ -2,7 +2,7 @@
 
 stdenv.mkDerivation rec {
   version = "1.1.1";
-  name = "itsx-${version}";
+  pname = "itsx";
 
   src = fetchurl {
     url = "http://microbiology.se/sw/ITSx_${version}.tar.gz";
diff --git a/pkgs/applications/science/biology/kallisto/default.nix b/pkgs/applications/science/biology/kallisto/default.nix
index d80ffea9a780..de93ae5d7829 100644
--- a/pkgs/applications/science/biology/kallisto/default.nix
+++ b/pkgs/applications/science/biology/kallisto/default.nix
@@ -1,25 +1,28 @@
-{ stdenv, fetchFromGitHub, cmake, hdf5, zlib }:
+{ stdenv, fetchFromGitHub, autoconf, cmake, hdf5, zlib }:
 
 stdenv.mkDerivation rec {
-  name = "kallisto-${version}";
-  version = "0.43.1";
+  pname = "kallisto";
+  version = "0.46.0";
 
   src = fetchFromGitHub {
     repo = "kallisto";
     owner = "pachterlab";
     rev = "v${version}";
-    sha256 = "04697pf7jvy7vw126s1rn09q4iab9223jvb1nb0jn7ilwkq7pgwz";
+    sha256 = "09vgdqwpigl4x3sdw5vjfyknsllkli339mh8xapbf7ldm0jldfn9";
   };
 
-  nativeBuildInputs = [ cmake ];
-  
+  nativeBuildInputs = [ autoconf cmake ];
+
   buildInputs = [ hdf5 zlib ];
 
+  # Parallel build fails in some cases: https://github.com/pachterlab/kallisto/issues/160
+  enableParallelBuilding = false;
+
   meta = with stdenv.lib; {
-    description = "kallisto is a program for quantifying abundances of transcripts from RNA-Seq data";
-    homepage = https://pachterlab.github.io/kallisto;
+    description = "Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data";
+    homepage = "https://pachterlab.github.io/kallisto";
     license = licenses.bsd2;
     platforms = platforms.linux;
-    maintainers = [ maintainers.arcadio ];
+    maintainers = with maintainers; [ arcadio ];
   };
 }
diff --git a/pkgs/applications/science/biology/messer-slim/default.nix b/pkgs/applications/science/biology/messer-slim/default.nix
index dbbf8d39a93c..d485666f3931 100644
--- a/pkgs/applications/science/biology/messer-slim/default.nix
+++ b/pkgs/applications/science/biology/messer-slim/default.nix
@@ -2,7 +2,7 @@
 
 stdenv.mkDerivation rec {
   version = "3.2.1"; 
-  name = "messer-slim-${version}";
+  pname = "messer-slim";
 
   src = fetchurl {
     url = "https://github.com/MesserLab/SLiM/archive/v${version}.tar.gz";
diff --git a/pkgs/applications/science/biology/minimap2/default.nix b/pkgs/applications/science/biology/minimap2/default.nix
index 84c65feb0937..bff2bcf428b5 100644
--- a/pkgs/applications/science/biology/minimap2/default.nix
+++ b/pkgs/applications/science/biology/minimap2/default.nix
@@ -1,7 +1,6 @@
 { stdenv, fetchFromGitHub, zlib }:
 
 stdenv.mkDerivation rec {
-  name = "${pname}-${version}";
   pname = "minimap2";
   version = "2.17";
 
diff --git a/pkgs/applications/science/biology/mosdepth/default.nix b/pkgs/applications/science/biology/mosdepth/default.nix
index 1bdb31616e4d..717b8c3ab2f3 100644
--- a/pkgs/applications/science/biology/mosdepth/default.nix
+++ b/pkgs/applications/science/biology/mosdepth/default.nix
@@ -16,7 +16,7 @@ let
   };
 
 in stdenv.mkDerivation rec {
-  name = "mosdepth-${version}";
+  pname = "mosdepth";
   version = "0.2.6";
 
   src = fetchFromGitHub {
diff --git a/pkgs/applications/science/biology/neuron/default.nix b/pkgs/applications/science/biology/neuron/default.nix
index 875e98499f53..4e6d3494c721 100644
--- a/pkgs/applications/science/biology/neuron/default.nix
+++ b/pkgs/applications/science/biology/neuron/default.nix
@@ -13,7 +13,7 @@
 }:
 
 stdenv.mkDerivation rec {
-  name = "neuron-${version}";
+  pname = "neuron";
   version = "7.5";
 
   nativeBuildInputs = [ which pkgconfig automake autoconf libtool ];
diff --git a/pkgs/applications/science/biology/niftyreg/default.nix b/pkgs/applications/science/biology/niftyreg/default.nix
index 9f1cb8db43d5..6379f2c32826 100644
--- a/pkgs/applications/science/biology/niftyreg/default.nix
+++ b/pkgs/applications/science/biology/niftyreg/default.nix
@@ -3,7 +3,6 @@
 stdenv.mkDerivation rec {
   pname   = "niftyreg";
   version = "1.3.9";
-  name    = "${pname}-${version}";
 
   src = fetchurl {
     url = "mirror://sourceforge/${pname}/nifty_reg-${version}/nifty_reg-${version}.tar.gz";
diff --git a/pkgs/applications/science/biology/niftyseg/default.nix b/pkgs/applications/science/biology/niftyseg/default.nix
index e7221855503c..689d3e42c979 100644
--- a/pkgs/applications/science/biology/niftyseg/default.nix
+++ b/pkgs/applications/science/biology/niftyseg/default.nix
@@ -3,7 +3,6 @@
 stdenv.mkDerivation rec {
   pname   = "niftyseg";
   version = "1.0";
-  name = "${pname}-${version}";
   src = fetchurl {
     url    = "https://github.com/KCL-BMEIS/NiftySeg/archive/v${version}.tar.gz";
     sha256 = "11q6yldsxp3k6gfp94c0xhcan2y3finzv8lzizmrc79yps3wjkn0";
diff --git a/pkgs/applications/science/biology/octopus/default.nix b/pkgs/applications/science/biology/octopus/default.nix
index 0a2074a06e97..9d81e08d7293 100644
--- a/pkgs/applications/science/biology/octopus/default.nix
+++ b/pkgs/applications/science/biology/octopus/default.nix
@@ -3,7 +3,6 @@
 stdenv.mkDerivation rec {
   pname = "octopus";
   version = "0.6.3-beta";
-  name = "${pname}-${version}";
 
   src = fetchFromGitHub {
     owner = "luntergroup";
diff --git a/pkgs/applications/science/biology/paml/default.nix b/pkgs/applications/science/biology/paml/default.nix
index 68efc2030e53..161188f7ef16 100644
--- a/pkgs/applications/science/biology/paml/default.nix
+++ b/pkgs/applications/science/biology/paml/default.nix
@@ -2,7 +2,7 @@
 
 stdenv.mkDerivation rec {
   version = "4.9i";
-  name = "paml-${version}";
+  pname = "paml";
   src = fetchurl {
     url = "http://abacus.gene.ucl.ac.uk/software/paml${version}.tgz";
     sha256 = "1k5lcyls6c33ppp5fxl8ply2fy7i2k0gcqaifsl7gnc81d8ay4dw";
diff --git a/pkgs/applications/science/biology/picard-tools/default.nix b/pkgs/applications/science/biology/picard-tools/default.nix
index e6a5ab741d94..2a57febe8f5d 100644
--- a/pkgs/applications/science/biology/picard-tools/default.nix
+++ b/pkgs/applications/science/biology/picard-tools/default.nix
@@ -1,7 +1,7 @@
 {stdenv, fetchurl, jre, makeWrapper}:
 
 stdenv.mkDerivation rec {
-  name = "picard-tools-${version}";
+  pname = "picard-tools";
   version = "2.20.5";
 
   src = fetchurl {
diff --git a/pkgs/applications/science/biology/platypus/default.nix b/pkgs/applications/science/biology/platypus/default.nix
index 323ca90f0a2a..fc6cfbb158c3 100644
--- a/pkgs/applications/science/biology/platypus/default.nix
+++ b/pkgs/applications/science/biology/platypus/default.nix
@@ -3,7 +3,7 @@
 let python = python27.withPackages (ps: with ps; [ cython ]);
 
 in stdenv.mkDerivation rec {
-  name = "platypus-unstable-${version}";
+  pname = "platypus-unstable";
   version = "2018-07-22";
 
   src = fetchFromGitHub {
diff --git a/pkgs/applications/science/biology/plink-ng/default.nix b/pkgs/applications/science/biology/plink-ng/default.nix
index 2efb59f536f6..52f8f70b7796 100644
--- a/pkgs/applications/science/biology/plink-ng/default.nix
+++ b/pkgs/applications/science/biology/plink-ng/default.nix
@@ -1,7 +1,7 @@
 { stdenv, fetchFromGitHub, zlib, openblas, darwin}:
 
 stdenv.mkDerivation rec {
-  name = "plink-ng-${version}";
+  pname = "plink-ng";
   version = "1.90b3";
 
   src = fetchFromGitHub {
diff --git a/pkgs/applications/science/biology/poretools/default.nix b/pkgs/applications/science/biology/poretools/default.nix
index 3bb9ea06fd46..8a19ae135e87 100755
--- a/pkgs/applications/science/biology/poretools/default.nix
+++ b/pkgs/applications/science/biology/poretools/default.nix
@@ -3,7 +3,6 @@
 pythonPackages.buildPythonPackage rec {
   pname = "poretools";
   version = "unstable-2016-07-10";
-  name = "${pname}-${version}";
 
   src = fetchFromGitHub {
     repo = pname;
diff --git a/pkgs/applications/science/biology/raxml/default.nix b/pkgs/applications/science/biology/raxml/default.nix
index 140f70323194..d7ee54bfbcf0 100644
--- a/pkgs/applications/science/biology/raxml/default.nix
+++ b/pkgs/applications/science/biology/raxml/default.nix
@@ -7,7 +7,6 @@
 stdenv.mkDerivation rec {
   pname = "RAxML";
   version = "8.2.12";
-  name = "${pname}-${version}";
 
   src = fetchFromGitHub {
     owner = "stamatak";
diff --git a/pkgs/applications/science/biology/samtools/default.nix b/pkgs/applications/science/biology/samtools/default.nix
index c4b4bb522c40..dd1a53472dbc 100644
--- a/pkgs/applications/science/biology/samtools/default.nix
+++ b/pkgs/applications/science/biology/samtools/default.nix
@@ -1,12 +1,11 @@
 { stdenv, fetchurl, zlib, htslib, perl, ncurses ? null }:
 
 stdenv.mkDerivation rec {
-  name = "${pname}-${version}";
   pname = "samtools";
   version = "1.9";
 
   src = fetchurl {
-    url = "https://github.com/samtools/samtools/releases/download/${version}/${name}.tar.bz2";
+    url = "https://github.com/samtools/samtools/releases/download/${version}/${pname}-${version}.tar.bz2";
     sha256 = "10ilqbmm7ri8z431sn90lvbjwizd0hhkf9rcqw8j823hf26nhgq8";
   };
 
diff --git a/pkgs/applications/science/biology/samtools/samtools_0_1_19.nix b/pkgs/applications/science/biology/samtools/samtools_0_1_19.nix
index a811bc4412f2..72d125ef8b6f 100644
--- a/pkgs/applications/science/biology/samtools/samtools_0_1_19.nix
+++ b/pkgs/applications/science/biology/samtools/samtools_0_1_19.nix
@@ -1,12 +1,11 @@
 { stdenv, fetchurl, zlib }:
 
 stdenv.mkDerivation rec {
-  name = "${pname}-${version}";
   pname = "samtools";
   version = "0.1.19";
 
   src = fetchurl {
-    url = "mirror://sourceforge/samtools/${name}.tar.bz2";
+    url = "mirror://sourceforge/samtools/${pname}-${version}.tar.bz2";
     sha256 = "d080c9d356e5f0ad334007e4461cbcee3c4ca97b8a7a5a48c44883cf9dee63d4";
   };
 
diff --git a/pkgs/applications/science/biology/seaview/default.nix b/pkgs/applications/science/biology/seaview/default.nix
index 17cf903ae49c..69dece88c276 100644
--- a/pkgs/applications/science/biology/seaview/default.nix
+++ b/pkgs/applications/science/biology/seaview/default.nix
@@ -2,7 +2,7 @@
 
 stdenv.mkDerivation rec {
   version = "4.7";
-  name = "seaview-${version}";
+  pname = "seaview";
 
   src = fetchurl {
     url = "ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_${version}.tar.gz";
diff --git a/pkgs/applications/science/biology/snpeff/default.nix b/pkgs/applications/science/biology/snpeff/default.nix
index dc2246903349..d700ee50a9c6 100644
--- a/pkgs/applications/science/biology/snpeff/default.nix
+++ b/pkgs/applications/science/biology/snpeff/default.nix
@@ -1,7 +1,7 @@
 {stdenv, fetchurl, jre, unzip, makeWrapper}:
 
 stdenv.mkDerivation rec {
-  name = "snpeff-${version}";
+  pname = "snpeff";
   version = "4.3t";
 
   src = fetchurl {
diff --git a/pkgs/applications/science/biology/somatic-sniper/default.nix b/pkgs/applications/science/biology/somatic-sniper/default.nix
index 4bbd6a320035..1961c71f43bb 100644
--- a/pkgs/applications/science/biology/somatic-sniper/default.nix
+++ b/pkgs/applications/science/biology/somatic-sniper/default.nix
@@ -1,7 +1,7 @@
 {stdenv, fetchFromGitHub, cmake, zlib, ncurses}:
 
 stdenv.mkDerivation rec {
-  name = "somatic-sniper-${version}";
+  pname = "somatic-sniper";
   version = "1.0.5.0";
 
   src = fetchFromGitHub {
diff --git a/pkgs/applications/science/biology/sortmerna/default.nix b/pkgs/applications/science/biology/sortmerna/default.nix
new file mode 100644
index 000000000000..4adce4461ede
--- /dev/null
+++ b/pkgs/applications/science/biology/sortmerna/default.nix
@@ -0,0 +1,38 @@
+{ stdenv, cmake, rocksdb, rapidjson, pkgconfig, fetchFromGitHub, fetchpatch, zlib }:
+
+stdenv.mkDerivation rec {
+  pname = "sortmerna";
+  version = "3.0.3";
+
+  src = fetchFromGitHub {
+    repo = pname;
+    owner = "biocore";
+    rev = "v${version}";
+    sha256 = "0zx5fbzyr8wdr0zwphp8hhcn1xz43s5lg2ag4py5sv0pv5l1jh76";
+  };
+
+  patches = [
+    (fetchpatch {
+      name = "CMakeInstallPrefix.patch";
+      url = "https://github.com/biocore/sortmerna/commit/4d36d620a3207e26cf3f588d4ec39889ea21eb79.patch";
+      sha256 = "0hc3jwdr6ylbyigg52q8islqc0mb1k8rrjadvjfqaxnili099apd";
+    })
+  ];
+
+  nativeBuildInputs = [ cmake rapidjson pkgconfig ];
+  buildInputs = [ zlib rocksdb rapidjson ];
+
+  cmakeFlags = [
+    "-DCMAKE_BUILD_TYPE=Release"
+    "-DROCKSDB_HOME=${rocksdb}"
+    "-DRAPIDJSON_HOME=${rapidjson}"
+  ];
+
+  meta = with stdenv.lib; {
+    description = "Tools for filtering, mapping, and OTU-picking from shotgun genomics data";
+    license = licenses.lgpl3;
+    platforms = platforms.x86_64;
+    homepage = https://bioinfo.lifl.fr/RNA/sortmerna/;
+    maintainers = with maintainers; [ luispedro ];
+  };
+}
diff --git a/pkgs/applications/science/biology/strelka/default.nix b/pkgs/applications/science/biology/strelka/default.nix
index e7f5eab8bfaf..84c90d895566 100644
--- a/pkgs/applications/science/biology/strelka/default.nix
+++ b/pkgs/applications/science/biology/strelka/default.nix
@@ -1,7 +1,7 @@
 {stdenv, fetchFromGitHub, cmake, zlib, python2}:
 
 stdenv.mkDerivation rec {
-  name = "strelka-${version}";
+  pname = "strelka";
   version = "2.9.10";
 
   src = fetchFromGitHub {
diff --git a/pkgs/applications/science/biology/trimal/default.nix b/pkgs/applications/science/biology/trimal/default.nix
new file mode 100755
index 000000000000..d4e8fee7bc36
--- /dev/null
+++ b/pkgs/applications/science/biology/trimal/default.nix
@@ -0,0 +1,31 @@
+{ stdenv, fetchFromGitHub }:
+
+stdenv.mkDerivation rec {
+  pname = "trimal";
+  version = "1.4.1";
+
+  src = fetchFromGitHub {
+    repo = pname;
+    owner = "scapella";
+    rev = "v${version}";
+    sha256 = "0isc7s3514di4z953xq53ncjkbi650sh4q9yyw5aag1n9hqnh7k0";
+  };
+
+  postUnpack = ''
+    sourceRoot=''${sourceRoot}/source
+    echo Source root reset to ''${sourceRoot}
+  '';
+
+  installPhase = ''
+    mkdir -p $out/bin
+    cp -a trimal readal statal $out/bin
+  '';
+
+  meta = with stdenv.lib; {
+    description = "A tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment";
+    license = licenses.gpl3;
+    platforms = platforms.linux;
+    homepage = http://trimal.cgenomics.org;
+    maintainers = [ maintainers.bzizou ];
+  };
+}
diff --git a/pkgs/applications/science/biology/varscan/default.nix b/pkgs/applications/science/biology/varscan/default.nix
index f685031e87e4..697a444193b1 100644
--- a/pkgs/applications/science/biology/varscan/default.nix
+++ b/pkgs/applications/science/biology/varscan/default.nix
@@ -1,7 +1,7 @@
 {stdenv, fetchurl, jre, makeWrapper}:
 
 stdenv.mkDerivation rec {
-  name = "varscan-${version}";
+  pname = "varscan";
   version = "2.4.2";
 
   src = fetchurl {
diff --git a/pkgs/applications/science/biology/vcftools/default.nix b/pkgs/applications/science/biology/vcftools/default.nix
index a6f52ae97b59..f6c9ad029c13 100755
--- a/pkgs/applications/science/biology/vcftools/default.nix
+++ b/pkgs/applications/science/biology/vcftools/default.nix
@@ -1,7 +1,6 @@
 { stdenv, fetchFromGitHub, zlib, autoreconfHook, pkgconfig, perl }:
 
 stdenv.mkDerivation rec {
-  name = "${pname}-${version}";
   pname = "vcftools";
   version = "0.1.16";