Merge branch 'develop'

.travis.yml

@@ -0,0 +1,12 @@
+language: nix
+services:
+  - docker
+env:
+  global:
+  - secure: IdGFh3a+MP47R7TGqRXJ7MLo3RWWgAX05zKHDmMkYRQbZMjcU5I3Ywu63pFEqiASvhwcdu0UjxLxReQAOLd+/ojyLjS+QQCLtrOLryyROa8DqP7Ci5f1CpZs0RYbXF6hPHOVlMoJ9T/DfEH0eQeuelQBG8Wr/0reigkwNdJi7x/zozIXGH/St2MgV3Qo6bQ2Xdkh3HbUL4zMGbjfqj/9x2lzWPAL5NKPMquSH2y76IsUJngBgHsQegAlnJb5TFMa2J53A6Kkl8lZQmD4nKOirRvqPJMiM1H3X44EKI9+woXWnXnPFz+KmQKhA9nShaqYcmZgWlJtLMtcMsknKrRaPNB21q69HtQjtOvHn9+FQnRvE6cMMFC6DIhsI7x3fKhU+EEeLsIrUSFPB62XTIqhqyuhwf7/4m/k6iL8oSRxEvVCqWKOPzjyGpqY50atKbdMMdkWAy+/NeenrRh6e92rin2m/d0Cwzs1tiknk9XdH/vNcCUjN000ePWnRgnKe01TeBBdVawOzWNQCBklxbW68shvdEu8ds/OYBUkAQDmlf4BjizlMvIRWbcaYfu3FyC8gopGeUX1d7tFBjD4eGOFGY99jPJG78l+z2BkVwhCZAD6wN/iglgtFy2mIRPF/+wLi75D9KRukhcaFF6nBLpyTTIhtse70EzNqC0cQjdSWjg= # DOCKER_USER
+  - secure: FLCsOdYx7pnXQ6AOjrAQN9WlvEqDio1Z1xeQ4l2DZb/kYPr+m/zpO/Ub7E2wGsTnEb8TRTycyk1Pm7gef7Ql81/W444WAauggICL0L2V294OK+ED/eKLn2UUvSsPicGtCNnW/VJeS4DsrzRvW/wnDXoXxH0Fx1AeeObvpqlt//TJEN+FRX79DjqPeT+PY47opUMPV8KMZjDkrjjmH4FnhawCE5licuE975p5NmqxsQ1c7afMI9/XntZisj2w6mdyF2rtmB2HE0uvg9rUSiTHlYnNQ6t40iKxE0fR3PaCi3pZwOmChJIprPzxit5mwW7PGy74WGKdivDb+G/iFyhxRS3EOyeHzUi0Wp4fHH8gsquKgprhn2v+qpqUa4of/pN2uffIMCc/TDDlkojy+P7GduPFwYbv2Ut3rW7VK3cpddYALPadeBSTTt55Dim7udM5e2bX+xz28mqrzHzV1sQSHkMalqk01KvfkAGhYgwogWhjP+NwkCKGRGhP8GOoYRP/vNW9/j3VSdKe78JKGDYKGgIaDu+ZmfhPeLykXo6QtIhlsjtU4wPR4Gb40sG6GoW04/54xXjbGd/X5dlDSISTKhi985TnA5ABu5iSm8m3S2jqioQYCu/A7YKo3okSDbdjvwPsEiusKStahy6ZHStJ4A6ndyZvb0de/yug+DLkgBI= # DOCKER_PASS
+before_script: docker login -u $DOCKER_USER -p $DOCKER_PASS
+script: ./buildContainers.sh
+branches:
+  only:
+  - develop

README.md

@@ -6,6 +6,11 @@ This can be used as a Git submodule to pin nixpkgs to a particular release and a
 ## Organization
 This repo tries to be minimal and thus does not include packages definitions from [NixOS/nixpkgs](https://github.com/NixOS/nixpkgs). Yet it follows the same folder structure so that customs packages added here can easily be copy pasted to a `NixOS/nixpkgs` fork to be included in the official nixpkgs release via pull requests. Custom packages added this way to the official Nix will be maintained there and removed from this repo.
 
+## New projects
+Copy `default.nix` and `shell.nix` into the root of your new project and add this repo as a git submodule.
+Edit `default.nix` so that the `pkgs` property matches the relative location of  `all-packages.nix`.
+Edit `shell.nix` so that the name and version are relevant to your project.
+
 ## Usage
 Edit `shell.nix` to adjust the name and version of your project to anything you want (optional).
 

buildContainers.sh

@@ -0,0 +1,19 @@
+#! /bin/bash
+source ./nixez.sh
+nixez install hello # To test and also get pinned Pkgs repo
+repo=bionode
+nixVersion=$(jq -r .version ./nixsrc.json)
+nix-env -f . -qaPA 'containerReadyPkgs' | awk '{print $2}' | while read pkg; do
+  echo "Checking if $pkg needs to be pushed to Docker Hubs"
+  pkgName=${pkg%%-*}
+  pkgVersion=${pkg##*-}
+  dockerTag="$pkgVersion"_nix"$nixVersion"
+  url="https://registry.hub.docker.com/v2/repositories/$repo/$pkgName/tags/"
+  if ! curl -s $url | jq -r '."results"[]["name"]' 2> /dev/null | grep -q -e "^$dockerTag$" ; then
+    echo "Building Docker image for $pkg"
+    nixez docker $pkgName
+    docker tag $repo/$pkgName:$dockerTag $repo/$pkgName:latest
+    echo "Pushing $pkg to Docker Hub"
+    docker push $repo/$pkgName
+  fi
+done

default.nix

@@ -1 +1,7 @@
-import ./pkgs/top-level/all-packages.nix
+{ system ? builtins.currentSystem, pkg ? null, timestamp ? "1970-01-01T00:00:01Z" }:
+let
+  nixpkgs = import <nixpkgs> { inherit system; };
+  makeOverridable = nixpkgs.stdenv.lib.makeOverridable;
+  pkgs = import ./pkgs/top-level/all-packages.nix;
+in
+  makeOverridable pkgs { inherit system; inherit timestamp; pkg = pkg; shellDir = ./shell.nix; }

lib/maintainers.nix

@@ -1,4 +1,5 @@
 { ...}:
 {
   bmpvieira = "Bruno Vieira <[email protected]>";
+  jbedo = "Justin Bedő <[email protected]>";
 }

nixbldOSX.sh

@@ -0,0 +1,20 @@
+#! /bin/bash -e
+
+dseditgroup -o create nixbld -q
+
+gid=$(dscl . -read /Groups/nixbld | awk '($1 == "PrimaryGroupID:") {print $2 }')
+
+echo "created nixbld group with gid $gid"
+
+for i in $(seq 1 10); do
+    user=/Users/nixbld$i
+    uid="$((30000 + $i))"
+    dscl . create $user
+    dscl . create $user RealName "Nix build user $i"
+    dscl . create $user PrimaryGroupID "$gid"
+    dscl . create $user UserShell /usr/bin/false
+    dscl . create $user NFSHomeDirectory /var/empty
+    dscl . create $user UniqueID "$uid"
+    dseditgroup -o edit -a nixbld$i -t user nixbld
+    echo "created nixbld$i user with uid $uid"
+done

nixez.fish

@@ -3,7 +3,7 @@
 # Usage: source ./nixez.fish
 
 function docker-load-nix
-  if test -n (cat /proc/version | grep Microsoft)
+  if grep -q -s Microsoft /proc/version
     set DIR (pwd | sed 's|/mnt/\(.\)|\1:|' | sed 's|/|\\\|g')
   else
     set DIR (pwd)
@@ -15,7 +15,7 @@ function docker-load-nix
     set ARGS -ti --rm
   end
 
-  docker run $ARGS -v $DIR:/data $IMAGE /bin/sh
+  # docker run $ARGS -v $DIR:/data $IMAGE
 end
 
 function read_confirm
@@ -45,10 +45,34 @@ function nixez
     nix-env -q
   case build
     nix-build (pwd) -A $argv[2]
+  case nodejs
+    cd pkgs/development/node-packages
+    node2nix -6 -i node-packages-v6.json -o node-packages-v6.nix -c composition-v6.nix
+    cd ../../..
   case docker
-    nix-build (pwd) -A dockerTar --argstr pkg $argv[2]
-    and docker-load-nix interactive
+    if uname -a | grep 'Darwin' >/dev/null
+      sudo (cat ~/.nixpkgs/linuxkit-builder/env) \
+      NIX_PATH="nixpkgs=$HOME/.nix-defexpr/channels/nixpkgs" \
+      nix-build (pwd) -A dockerTar --argstr pkg $argv[2] \
+        --argstr timestamp (date -u +"%Y-%m-%dT%H:%M:%SZ") \
+        --argstr system "x86_64-linux"
+    else
+      nix-build (pwd) -A dockerTar --argstr pkg $argv[2] \
+        --argstr timestamp (date -u +"%Y-%m-%dT%H:%M:%SZ")
+    end
+    if [ -t 1 ]
+      docker-load-nix interactive
+    else
+      docker-load-nix
+    end
   case singularity
+    sudo (cat ~/.nixpkgs/linuxkit-builder/env) \
+    NIX_PATH="nixpkgs=$HOME/.nix-defexpr/channels/nixpkgs" \
+    nix-build (pwd) -A dockerTar --argstr pkg $argv[2]
+    and docker-load-nix
+    set NAME (docker ps -l --format "{{.Image}}" | sed 's|:|_|')
+    and docker export (docker ps -lq) | gzip > $NAME.tar.gz
+  case singularity-mac
     nix-build (pwd) -A dockerTar --argstr pkg $argv[2]
     and docker-load-nix
     set NAME (docker ps -l --format "{{.Image}}" | sed 's|:|_|')
@@ -66,6 +90,8 @@ function nixez
     if read_confirm
       curl https://nixos.org/nix/install | sh
     end
+  case repair
+    nix-store --verify --check-contents
   case '*'
     echo "Options: shell, search, install, remove, list, build, docker, singularity, setup, unsafe-setup"
   end

nixez.sh

@@ -3,7 +3,7 @@
 # Usage: source ./nixez.sh
 
 function docker-load-nix() {
-  if grep -q Microsoft /proc/version; then
+  if grep -q -s Microsoft /proc/version; then
     DIR=$(pwd | sed 's|/mnt/\(.\)|\1:|' | sed 's|/|\\|g')
   else
     DIR=$(pwd)
@@ -17,7 +17,7 @@ function docker-load-nix() {
     ARGS=""
   fi
 
-  docker run $ARGS -v "$DIR:/data" "$IMAGE" /bin/sh
+  # docker run $ARGS -v "$DIR:/data" "$IMAGE"
 }
 
 function nixez() {
@@ -28,9 +28,31 @@ function nixez() {
     remove) nix-env -e "$2" ;;
     list) nix-env -q;;
     build) nix-build "$(pwd)" -A "$2" ;;
+    nodejs)
+      cd pkgs/development/node-packages
+      node2nix -6 -i node-packages-v6.json -o node-packages-v6.nix -c composition-v6.nix
+      cd ../../..
+    ;;
     docker)
+      if [ "$(uname)" == "Darwin" ]; then
+        sudo $(cat ~/.nixpkgs/linuxkit-builder/env) \
+        NIX_PATH="nixpkgs=$HOME/.nix-defexpr/channels/nixpkgs" \
+        nix-build "$(pwd)" -A dockerTar --argstr pkg "$2" \
+          --argstr timestamp $(date -u +"%Y-%m-%dT%H:%M:%SZ") \
+          --argstr system "x86_64-linux"
+      else
+        nix-build "$(pwd)" -A dockerTar --argstr pkg "$2" \
+          --argstr timestamp $(date -u +"%Y-%m-%dT%H:%M:%SZ")
+      fi
+      if [ -t 0 ]; then
+        docker-load-nix interactive
+      else
+        docker-load-nix
+      fi
+    ;;
+    docker-push)
       nix-build "$(pwd)" -A dockerTar --argstr pkg "$2" &&
-      docker-load-nix interactive
+      docker-load-nix
     ;;
     singularity)
       nix-build "$(pwd)" -A dockerTar --argstr pkg "$2" &&
@@ -63,6 +85,9 @@ function nixez() {
         ;;
       esac
     ;;
+    repair)
+      nix-store --verify --check-contents
+    ;;
     * ) echo "Options: shell, search, install, remove, list, build, docker, singularity" ;;
   esac
 }

nixsrc.json

@@ -1,9 +1,9 @@
 {
-  "version": "17.09-beta",
+  "version": "17.09",
   "origin": {
     "owner": "NixOS",
     "repo": "nixpkgs",
-    "rev": "6a7066eb53685438564dc50362666d0e7f150110",
-    "sha256": "1psff8lpp5kmihsg7xv46a0d3rmhsb4kyb9w8r213gn8ggigwg57"
+    "rev": "39cd40f7bea40116ecb756d46a687bfd0d2e550e",
+    "sha256": "0kpx4h9p1lhjbn1gsil111swa62hmjs9g93xmsavfiki910s73sh"
   }
 }

pkgs/applications/science/biology/bcftools/default.nix

@@ -0,0 +1,29 @@
+{ stdenv, fetchurl, htslib, zlib, bzip2, lzma, curl, perl, bash }:
+
+stdenv.mkDerivation rec {
+  name = "${pname}-${version}";
+  pname = "bcftools";
+  upstreamVersion = "1.6";
+  version = "${upstreamVersion}noperl";
+
+  src = fetchurl {
+    url = "https://github.com/samtools/bcftools/releases/download/${upstreamVersion}/${pname}-${upstreamVersion}.tar.bz2";
+    sha256 = "10prgmf09a13mk18840938ijqgfc9y92hfc7sa2gcv07ddri0c19";
+  };
+
+  buildInputs = [ htslib zlib bzip2 lzma curl ];
+
+  makeFlags = [
+    "HSTDIR=${htslib}"
+    "prefix=$(out)"
+    "CC=cc"
+  ];
+
+  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 ];
+  };
+}

pkgs/applications/science/biology/bedtools/default.nix

@@ -0,0 +1,26 @@
+{stdenv, fetchFromGitHub, zlib, python}:
+
+stdenv.mkDerivation rec {
+  name = "bedtools-${version}";
+  version = "2.26.0";
+
+  src = fetchFromGitHub {
+    owner = "arq5x";
+    repo = "bedtools2";
+    rev = "v${version}";
+    sha256 = "1j2ia68rmcw3qksjm5gvv1cb84bh76vmln59mvncr2an23f5a3ss";
+  };
+
+  buildInputs = [ zlib python ];
+  cc = if stdenv.cc.isClang then "clang++" else "g++";
+  buildPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cc} -j $NIX_BUILD_CORES";
+  installPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cc} install";
+
+  meta = with stdenv.lib; {
+    description = "A powerful toolset for genome arithmetic.";
+    license = licenses.gpl2;
+    homepage = https://bedtools.readthedocs.io/en/latest/;
+    maintainers = with maintainers; [ jbedo ];
+    platforms = platforms.unix;
+  };
+}

pkgs/applications/science/biology/bowtie2/default.nix

@@ -0,0 +1,26 @@
+{ stdenv, fetchFromGitHub, zlib, tbb }:
+
+stdenv.mkDerivation rec {
+  pname = "bowtie2";
+  version = "2.3.3.1";
+  name = "${pname}-${version}";
+
+  src = fetchFromGitHub {
+    owner = "BenLangmead";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "1pcyks76bnnkq6h0gqjw4fkdddjjnw7k5ibim7ajkbvfw58a99y0";
+  };
+
+  buildInputs = [ zlib tbb ];
+
+  installFlags = [ "prefix=$(out)" ];
+
+  meta = with stdenv.lib; {
+    description = "An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences";
+    license = licenses.gpl3;
+    homepage = http://bowtie-bio.sf.net/bowtie2;
+    maintainers = with maintainers; [ rybern ];
+    platforms = platforms.all;
+  };
+}

pkgs/applications/science/biology/bwa/default.nix

@@ -0,0 +1,25 @@
+{ stdenv, fetchurl, zlib }:
+
+stdenv.mkDerivation rec {
+  name    = "bwa-${version}";
+  version = "0.7.16a";
+
+  src = fetchurl {
+    url = "mirror://sourceforge/bio-bwa/${name}.tar.bz2";
+    sha256 = "0w61zxh6b4isydw5qp6pdb1mc50jg1h8vhahw2xm24w7i1gxpv4g";
+  };
+
+  buildInputs = [ zlib ];
+
+  installPhase = ''
+    install -vD bwa $out/bin/bwa
+  '';
+
+  meta = with stdenv.lib; {
+    description = "A software package for mapping low-divergent sequences against a large reference genome, such as the human genome";
+    license     = licenses.gpl3;
+    homepage    = http://bio-bwa.sourceforge.net/;
+    maintainers = with maintainers; [ luispedro ];
+    platforms = [ "x86_64-linux" ];
+  };
+}

pkgs/applications/science/biology/fastqc/default.nix

@@ -1,8 +1,9 @@
 { stdenv, fetchurl, unzip, jre }:
 
 stdenv.mkDerivation rec {
-  name = "fastqc-${version}";
+  pname = "fastqc";
   version = "0.11.5";
+  name = "${pname}-${version}";
 
   src = fetchurl {
     url = "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v${version}.zip";

pkgs/applications/science/biology/freebayes/default.nix

@@ -0,0 +1,29 @@
+{ stdenv, fetchFromGitHub, cmake, gcc, zlib, bzip2, lzma }:
+
+stdenv.mkDerivation rec {
+  name    = "freebayes-${version}";
+  version = "2017-08-23";
+
+  src = fetchFromGitHub {
+    name = "freebayes-${version}-src";
+    owner  = "ekg";
+    repo   = "freebayes";
+    rev    = "8d2b3a060da473e1f4f89be04edfce5cba63f1d3";
+    sha256 = "0yyrgk2639lz1yvg4jf0ccahnkic31dy77q05pb3i28rjf37v45z";
+    fetchSubmodules = true;
+  };
+
+  buildInputs = [ zlib bzip2 lzma ];
+
+  installPhase = ''
+    install -vD bin/freebayes bin/bamleftalign scripts/* -t $out/bin
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Bayesian haplotype-based polymorphism discovery and genotyping";
+    license     = licenses.mit;
+    homepage    = https://github.com/ekg/freebayes;
+    maintainers = with maintainers; [ jdagilliland ];
+    platforms = [ "x86_64-linux" ];
+  };
+}