large refactor

- use bionix.pkgs instead of nixpkgs
- replace stdenv.mkDerivation with stage

51 files changed, 186 insertions, 267 deletions

diff --git a/default.nix b/default.nix
index 6ddcd1b..c50e063 100644
--- a/default.nix
+++ b/default.nix
@@ -4,7 +4,7 @@ let
   inherit (nixpkgs) fetchurl callPackage;
 
   bionix = nixpkgs.lib.makeExtensible (self:
-  let callBionix = file: attrs: import file ({ bionix = self; nixpkgs = nixpkgs; } // attrs);
+  let callBionix = file: attrs: import file ({ bionix = self; } // attrs);
   in with self; {
     callBionix = callBionix;
     id = x: x;
@@ -60,8 +60,8 @@ let
 
     # Export nixpkgs and standard library lib
     pkgs = nixpkgs;
-    lib = nixpkgs.lib;
-    stage = nixpkgs.stdenvNoCC.mkDerivation;
+    lib = nixpkgs.lib // { types = types; };
+    stage = nixpkgs.stdenv.mkDerivation;
 
     # splitting/joining
     splitFile = file: drv: stage {
diff --git a/lib/references.nix b/lib/references.nix
index 9d1b947..2e5e937 100755
--- a/lib/references.nix
+++ b/lib/references.nix
@@ -1,33 +1,33 @@
-{ bionix, nixpkgs }:
+{ bionix }:
 
-with nixpkgs;
-with bionix.types;
+with bionix;
+with types;
 
 rec {
   grch38 = grch38-p12;
   grch38-p12 = rec {
-    seq = stdenvNoCC.mkDerivation rec {
+    seq = pkgs.stdenvNoCC.mkDerivation rec {
       name = "seq-grch38.${version}";
       version = "p12";
-      src = fetchurl {
+      src = pkgs.fetchurl {
         url = "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_28/GRCh38.p12.genome.fa.gz";
         sha256 = "0ji2ggpmgnbpwbhq8mirj6h3lyy02nl2rnz7n892iq5cqpsblh4z";
       };
       buildCommand = "gunzip < $src > $out";
       passthru.filetype = filetype.fa {};
     };
-    blacklist = stdenvNoCC.mkDerivation {
+    blacklist = pkgs.stdenvNoCC.mkDerivation {
       name = "blacklist-grch38";
-      src = fetchurl {
+      src = pkgs.fetchurl {
         url = "http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38-human/hg38.blacklist.bed.gz";
         sha256 = "1lpnqq1mjidbdxj5i6x26rxa8x1rs8q3hlf0z1z49j3jsnkgffky";
       };
       buildCommand = "gunzip < $src > $out";
       passthru.filetype = filetype.bed { ref = seq; };
     };
-    dbsnp = stdenvNoCC.mkDerivation {
+    dbsnp = pkgs.stdenvNoCC.mkDerivation {
       name = "dbsnp-b151_GRCh38p7";
-      src = fetchurl {
+      src = pkgs.fetchurl {
         url = "ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/common_all_20180418.vcf.gz";
         sha256 = "0r6m2yrcfw8bbdca515axjls30ssjas6x3qwi5qz07l3prjwmdd4";
       };
@@ -37,7 +37,7 @@ rec {
         '';
         passthru.filetype = filetype.vcf { ref = seq; };
       };
-      cosmic = {coding, noncoding}: stdenvNoCC.mkDerivation rec {
+      cosmic = {coding, noncoding}: pkgs.stdenvNoCC.mkDerivation rec {
         name = "cosmic-grch38";
         buildInputs = [ gawk ];
         buildCommand = ''
@@ -47,20 +47,20 @@ rec {
         passthru.filetype = filetype.vcf { ref = seq; };
       };
       ensembl = {
-        cdna = stdenvNoCC.mkDerivation rec {
+        cdna = pkgs.stdenvNoCC.mkDerivation rec {
           name = "ensembl-grch38-cdna-${version}";
           version = "94";
-          src = fetchurl {
+          src = pkgs.fetchurl {
             url = "ftp://ftp.ensembl.org/pub/release-${version}/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz";
             sha256 = "1fc5d6p2wlwsm49wnmxmm3byjx5jvr6z9fpzrq7v7fpb086adl0h";
           };
           buildCommand = "gunzip < $src > $out";
           passthru.filetype = filetype.fa {};
         };
-        ncrna = stdenvNoCC.mkDerivation rec {
+        ncrna = pkgs.stdenvNoCC.mkDerivation rec {
           name = "ensembl-grch38-ncrna-${version}";
           version = "94";
-          src = fetchurl {
+          src = pkgs.fetchurl {
             url = "ftp://ftp.ensembl.org/pub/release-${version}/fasta/homo_sapiens/ncrna/Homo_sapiens.GRCh38.ncrna.fa.gz";
             sha256 = "1cpasykwriila52nqgvw6d3mjyh6d9qi613hvhn4h1dxkqzgnjff";
           };
@@ -71,7 +71,7 @@ rec {
       snpeff = {
         db = stdenv.mkDerivation rec {
           name = "GRCh38.86";
-          src = fetchurl {
+          src = pkgs.fetchurl {
             url = "mirror://sourceforge/project/snpeff/databases/v4_3/snpEff_v4_3_${name}.zip";
             sha256 = "1rf8q7l732ayjq2lpny4s75zpij05j00151374nqblk4wri2mz0i";
           };
@@ -98,10 +98,10 @@ rec {
 
     grcm38 = grcm38-p6;
     grcm38-p6 = {
-      seq = stdenvNoCC.mkDerivation rec {
+      seq = pkgs.stdenvNoCC.mkDerivation rec {
         name = "seq-grcm38.${version}";
         version = "p6";
-        src = fetchurl {
+        src = pkgs.fetchurl {
           url = "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M19/GRCm38.${version}.genome.fa.gz";
           sha256 = "0ryiqab5bldpzawylsk2qpjxr2j701q03ww9jqyxhkimqpn9g3mr";
         };
@@ -109,20 +109,20 @@ rec {
         passthru.filetype = filetype.fa {};
       };
       ensembl = {
-        cdna = stdenvNoCC.mkDerivation rec {
+        cdna = pkgs.stdenvNoCC.mkDerivation rec {
           name = "ensembl-grch38-cdna-${version}";
           version = "94";
-          src = fetchurl {
+          src = pkgs.fetchurl {
             url = "ftp://ftp.ensembl.org/pub/release-${version}/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz";
             sha256 = "0khp9l6s35lav2xqp7vkk6ybnz4wjihn7lapjf2lbpnbzjb4hp6d";
           };
           buildCommand = "gunzip < $src > $out";
           passthru.filetype = filetype.fa {};
         };
-        ncrna = stdenvNoCC.mkDerivation rec {
+        ncrna = pkgs.stdenvNoCC.mkDerivation rec {
           name = "ensembl-grch38-ncrna-${version}";
           version = "94";
-          src = fetchurl {
+          src = pkgs.fetchurl {
             url = "ftp://ftp.ensembl.org/pub/release-${version}/fasta/mus_musculus/ncrna/Mus_musculus.GRCm38.ncrna.fa.gz";
             sha256 = "0d997gm8p2b89rm5d46m2x4vz9lijxarfr2lzylnbi8gyqrbagdd";
           };
@@ -134,10 +134,10 @@ rec {
 
     mm10 = mm10-p4;
     mm10-p4 = {
-      seq = stdenvNoCC.mkDerivation rec {
+      seq = pkgs.stdenvNoCC.mkDerivation rec {
         name = "seq-mm10.${version}";
         version = "p4";
-        src = fetchurl {
+        src = pkgs.fetchurl {
           url = "http://hgdownload.soe.ucsc.edu/goldenPath/mm10/mm10Patch4/mm10Patch4.fa.gz";
           sha256 = "1660d6d05f3aa266c6053cfd1efef1747d9e854836917241d6f47cff7a55340c";
         };
diff --git a/lib/types.nix b/lib/types.nix
index 3e26b8a..f711170 100644
--- a/lib/types.nix
+++ b/lib/types.nix
@@ -1,10 +1,10 @@
-{bionix, nixpkgs}:
+{bionix}:
 
-with nixpkgs;
+with bionix;
 with lib;
 
 let
-  nix-adt-src = fetchFromGitHub {
+  nix-adt-src = pkgs.fetchFromGitHub {
     owner = "shlevy";
     repo = "nix-adt";
     rev = "dd04b5d08eed65ecd73aafde56a78078e09f1c74";
diff --git a/test-tnpair.nix b/test-tnpair.nix
index b897366..0851a74 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -1,49 +1,39 @@
-with (import <nixpkgs> {});
+with import <bionix> {};
 with lib;
 
 let
-  bionix = (import <bionix> {}).extend (self: super: with self; {
-    bwa = with super.bwa; {
-      align = align;
-      index = def index { flags = "-a is"; };
-    };
-  });
-
-in
-
-with bionix;
-
-let
-  fetchlocal = path: stdenv.mkDerivation {
+  fetchlocal = path: pkgs.stdenv.mkDerivation {
     name = baseNameOf path;
     buildCommand = "ln -s ${path} $out";
   };
   fetchfq = attrs: types.tagFiletype (types.filetype.fq {}) (fetchlocal attrs);
   fetchfa = attrs: types.tagFiletype (types.filetype.fa {}) (fetchlocal attrs);
 
-  ref = fetchfa ./example/ref.fa;
+  ref = fetchfa ./examples/ref.fa;
 
   alignWithRG = rg: bwa.align { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";};
   sort = samtools.sort {};
   flagstat = samtools.flagstat {};
   check = fastqc.check {};
   callVariants = strelka.call {};
+  markdup = samtools.markdup {};
+  fixmate = samtools.fixmate {};
 
   tnpair = {
     tumour = {name = "mysample1"; files = {
-        input1 = fetchfq ./example/sample1-1.fq;
-        input2 = fetchfq ./example/sample1-2.fq;
+        input1 = fetchfq ./examples/sample1-1.fq;
+        input2 = fetchfq ./examples/sample1-2.fq;
       };
     };
     normal = {name = "mysample2"; files = {
-        input1 = fetchfq ./example/sample2-1.fq;
-        input2 = fetchfq ./example/sample2-2.fq;
+        input1 = fetchfq ./examples/sample2-1.fq;
+        input2 = fetchfq ./examples/sample2-2.fq;
       };
     };
   };
 
   processPair = { tumour, normal }: rec {
-    alignments = mapAttrs (_: x: sort (alignWithRG x.name x.files)) { inherit normal tumour; };
+    alignments = mapAttrs (_: x: markdup (sort (fixmate (alignWithRG x.name x.files)))) { inherit normal tumour; };
     variants = callVariants alignments;
   };
 
diff --git a/test.nix b/test.nix
deleted file mode 100644
index 9851310..0000000
--- a/test.nix
+++ /dev/null
@@ -1,35 +0,0 @@
-{pkgs ? import <nixpkgs> {}
-,bionix ? import <bionix> {}}:
-
-with pkgs;
-with lib;
-with bionix;
-
-let
-  inherit (types) filetype tagFiletype;
-
-  fetchLocal = path: stdenv.mkDerivation {
-    name = baseNameOf path;
-    buildCommand = "ln -s ${path} $out";
-  };
-  tagfq = path: tagFiletype (filetype.fq {}) (fetchLocal path);
-  tagfa = path: tagFiletype (filetype.fa {}) (fetchLocal path);
-
-  ref = tagfa ./example/ref.fa;
-  alignWithRG = rg: bwa.align { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";};
-
-  samples = [ {name = "mysample1"; files = {input1 = tagfq ./example/sample1-1.fq; input2 = tagfq ./example/sample1-2.fq;};}
-              {name = "mysample2"; files = {input1 = tagfq ./example/sample2-1.fq; input2 = tagfq ./example/sample2-1.fq;};} ];
-
-  alignments = map (i: samtools.sort {} (alignWithRG i.name i.files)) samples;
-  variants = platypus.call {} alignments;
-
-in stdenv.mkDerivation {
-  name = "myproject";
-  buildCommand = ''
-    mkdir $out
-    ln -s ${variants} $out/platypus.vcf
-    mkdir $out/alignments
-    ${concatStringsSep "\n" (zipListsWith (s: a: "ln -s ${a} $out/alignments/${s.name}.bam") samples alignments)}
-  '';
-}
diff --git a/tools/bowtie-align.nix b/tools/bowtie-align.nix
index 456747a..67a1169 100644
--- a/tools/bowtie-align.nix
+++ b/tools/bowtie-align.nix
@@ -1,5 +1,4 @@
 { bionix
-, nixpkgs
 , ref
 , bamOutput ? true
 , flags ? null
@@ -10,18 +9,18 @@
 , input2 ? null
 }:
 
-with nixpkgs;
+with bionix;
 with lib;
-with bionix.types;
-with bionix.compression;
+with types;
+with compression;
 
 let
   fa = f: matchFiletype "bowtie2-ref" { fa = _: f; } f;
   fq = f: matchFiletype "bowtie2-input" { fq = _: f; gz = matchFiletype' "bowtie2-input" { fq = _: f; }; } f;
 
-in stdenv.mkDerivation {
+in stage {
   name = "bowtie2-align";
-  buildInputs = [ bowtie2 bc ] ++ optional bamOutput samtools;
+  buildInputs = with pkgs; [ bowtie2 bc ] ++ optional bamOutput samtools;
   buildCommand = ''
     cores=$(echo $NIX_BUILD_CORES ${optionalString bamOutput "- 1"} | bc)
     if [[ $cores -lt 1 ]] ; then
diff --git a/tools/bowtie-index.nix b/tools/bowtie-index.nix
index 98e529f..4554ad1 100644
--- a/tools/bowtie-index.nix
+++ b/tools/bowtie-index.nix
@@ -1,20 +1,19 @@
 { bionix
-, nixpkgs
 , flags ? null
 , seed ? 42
 }:
 
 ref:
 
-with nixpkgs;
+with bionix;
 with lib;
-with bionix.types;
+with types;
 
 assert (matchFiletype "bowtie-index" { fa = _: true; } ref);
 
-stdenv.mkDerivation {
+stage {
   name = "bowtie-index";
-  buildInputs = [ bowtie2 ];
+  buildInputs = with pkgs; [ bowtie2 ];
   buildCommand = ''
     mkdir $out
     bowtie2-build --seed ${toString seed} --threads $NIX_BUILD_CORES ${optionalString (flags != null) flags} ${ref} $out/ref
diff --git a/tools/bowtie.nix b/tools/bowtie.nix
index df8f955..a4439d3 100644
--- a/tools/bowtie.nix
+++ b/tools/bowtie.nix
@@ -1,4 +1,4 @@
-{ bionix, nixpkgs }:
+{ bionix }:
 
 with bionix;
 
diff --git a/tools/bwa-index.nix b/tools/bwa-index.nix
index c879bc4..17b651f 100644
--- a/tools/bwa-index.nix
+++ b/tools/bwa-index.nix
@@ -1,19 +1,18 @@
 { bionix
-, nixpkgs
 , flags ? null
 }:
 
 ref:
 
-with nixpkgs;
+with bionix;
 with lib;
-with bionix.types;
+with types;
 
 assert (matchFiletype "bwa-index" { fa = _: true; } ref);
 
-stdenv.mkDerivation {
+stage {
   name = "bwa-index";
-  buildInputs = [ bwa ];
+  buildInputs = with pkgs; [ bwa ];
   buildCommand = ''
     ln -s ${ref} ref.fa
     bwa index ${optionalString (flags != null) flags} ref.fa
diff --git a/tools/bwa-mem.nix b/tools/bwa-mem.nix
index 2b3bc64..1427b49 100644
--- a/tools/bwa-mem.nix
+++ b/tools/bwa-mem.nix
@@ -1,5 +1,4 @@
 { bionix
-, nixpkgs
 , ref
 , bamOutput ? true
 , flags ? null
@@ -10,18 +9,18 @@
 , input2 ? null
 }:
 
-with nixpkgs;
+with bionix;
 with lib;
-with bionix.types;
-with bionix.compression;
+with types;
+with compression;
 
 let
   fa = f: matchFiletype "bwa-ref" { fa = _: f; } f;
   fq = f: matchFiletype "bwa-input" { fq = _: f; gz = matchFiletype' "bwa-input" { fq = _: f; }; } f;
 
-in stdenv.mkDerivation {
+in stage {
   name = "bwa-mem";
-  buildInputs = [ bwa bc ] ++ optional bamOutput samtools;
+  buildInputs = with pkgs; [ bwa bc ] ++ optional bamOutput samtools;
   buildCommand = ''
     ln -s ${fa ref} ref.fa
     for f in ${bionix.bwa.index indexAttrs ref}/* ; do
diff --git a/tools/bwa.nix b/tools/bwa.nix
index ea0e6a0..d0ab5ee 100644
--- a/tools/bwa.nix
+++ b/tools/bwa.nix
@@ -1,4 +1,4 @@
-{ bionix, nixpkgs }:
+{ bionix }:
 
 with bionix;
 
diff --git a/tools/compression.nix b/tools/compression.nix
index 4184fec..6e69d7e 100644
--- a/tools/compression.nix
+++ b/tools/compression.nix
@@ -1,6 +1,5 @@
-{bionix, nixpkgs}:
+{bionix}:
 
-with nixpkgs;
 with bionix;
 
 {
@@ -12,11 +11,11 @@ with bionix;
     cram = _: f;
     vcf = _: f;
     bed = _: f;
-    gz = _: types.tagFiletype (types.gunzip f.filetype) (stdenv.mkDerivation {
+    gz = _: types.tagFiletype (types.gunzip f.filetype) (stage {
       name = "gunzip";
       buildCommand = "gunzip < ${f} > $out";
     });
-    bz2 = _: types.tagFiletype (types.bunzip2 f.filetype) (stdenv.mkDerivation {
+    bz2 = _: types.tagFiletype (types.bunzip2 f.filetype) (stage {
       name = "bunzip2";
       buildCommand = "bunzip2 < ${f} > $out";
     });
@@ -24,7 +23,7 @@ with bionix;
 
   gzip = f:
     let
-      gz = (stdenv.mkDerivation {
+      gz = (stage {
         name = "gzip";
         buildCommand = "gzip < ${f} > $out";
         passthru = { filetype = types.filetype.gz f.filetype; };
@@ -42,7 +41,7 @@ with bionix;
 
   bzip2 = f:
     let
-      bz2 = (stdenv.mkDerivation {
+      bz2 = (stage {
         name = "bzip2";
         buildCommand = "bzip2 < ${f} > $out";
         passthru = { filetype = types.filetype.bz2 f.filetype; };
diff --git a/tools/crumble.nix b/tools/crumble.nix
index 6031fca..4256f37 100644
--- a/tools/crumble.nix
+++ b/tools/crumble.nix
@@ -1,8 +1,7 @@
-{ bionix, nixpkgs }:
+{ bionix }:
 
-with nixpkgs;
 with bionix;
 
 {
-  crumble = callPackage ./crumble-app.nix {};
+  crumble = pkgs.callPackage ./crumble-app.nix {};
 }
diff --git a/tools/fastqc-check.nix b/tools/fastqc-check.nix
index 17d6183..d33b987 100644
--- a/tools/fastqc-check.nix
+++ b/tools/fastqc-check.nix
@@ -1,14 +1,13 @@
 { bionix
-, nixpkgs
 , flags ? null
 }:
 
-with nixpkgs;
+with bionix;
 with lib;
 
 input:
 
-stdenv.mkDerivation {
+stage {
   name = "fastqc-check";
   buildInputs = [ bionix.fastqc.fastqc ];
   buildCommand = ''
diff --git a/tools/fastqc.nix b/tools/fastqc.nix
index 6e603b2..5632958 100644
--- a/tools/fastqc.nix
+++ b/tools/fastqc.nix
@@ -1,9 +1,8 @@
-{ bionix, nixpkgs }:
+{ bionix }:
 
-with nixpkgs;
 with bionix;
 
 {
-  fastqc = callPackage ./fastqc-app.nix {};
+  fastqc = pkgs.callPackage ./fastqc-app.nix {};
   check = callBionixE ./fastqc-check.nix;
 }
diff --git a/tools/gridss-assemble.nix b/tools/gridss-assemble.nix
index f57bc12..e5cb3ca 100644
--- a/tools/gridss-assemble.nix
+++ b/tools/gridss-assemble.nix
@@ -1,5 +1,4 @@
 { bionix
-, nixpkgs
 , bwaIndexAttrs ? {}
 , faidxAttrs ? {}
 , indexAttrs ? {}
@@ -9,9 +8,9 @@
 , heapSize ? "31g"
 }:
 
-with nixpkgs;
+with bionix;
 with lib;
-with bionix.types;
+with types;
 
 inputs:
 
@@ -36,9 +35,9 @@ in
 assert (all sorted inputs);
 assert (homoRef);
 
-stdenv.mkDerivation rec {
+stage rec {
   name = "gridss-assemble";
-  buildInputs = [ jre bwa ];
+  buildInputs = with pkgs; [ jre bwa ];
   buildCommand = ''
     TMPDIR=$(pwd)
     ln -s ${ref} ref.fa
diff --git a/tools/gridss-callVariants.nix b/tools/gridss-callVariants.nix
index d55db23..4117126 100644
--- a/tools/gridss-callVariants.nix
+++ b/tools/gridss-callVariants.nix
@@ -1,5 +1,4 @@
 { bionix
-, nixpkgs
 , blacklist ? null
 , bwaIndexAttrs ? {}
 , faidxAttrs ? {}
@@ -8,9 +7,9 @@
 , heapSize ? "31g"
 }:
 
-with nixpkgs;
+with bionix;
 with lib;
-with bionix.types;
+with types;
 
 inputs:
 
@@ -22,9 +21,9 @@ in
 
 assert (length (unique refs) == 1);
 
-stdenv.mkDerivation rec {
+stage rec {
   name = "gridss-callVariants";
-  buildInputs = [ jre R bwa ];
+  buildInputs = with pkgs; [ jre R bwa ];
   buildCommand = ''
     ln -s ${ref} ref.fa
     ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai
diff --git a/tools/gridss-collectMetrics.nix b/tools/gridss-collectMetrics.nix
index 17e3c46..37e22f1 100644
--- a/tools/gridss-collectMetrics.nix
+++ b/tools/gridss-collectMetrics.nix
@@ -1,14 +1,13 @@
 { bionix
-, nixpkgs
 , thresholdCoverage ? 10000
 , flags ? null
 , config ? null
 , heapSize ? "1G"
 }:
 
-with nixpkgs;
+with bionix;
 with lib;
-with bionix.types;
+with types;
 
 input:
 
@@ -17,9 +16,9 @@ let
 in
 
 
-stdenv.mkDerivation rec {
+stage rec {
   name = "gridss-collectMetrics";
-  buildInputs = [ jre R ];
+  buildInputs = with pkgs; [ jre R ];
   buildCommand = ''
     mkdir $out
     java -Xmx${heapSize} -cp ${bionix.gridss.jar} \
diff --git a/tools/gridss-computeSamTags.nix b/tools/gridss-computeSamTags.nix
index c462461..5b249e7 100644
--- a/tools/gridss-computeSamTags.nix
+++ b/tools/gridss-computeSamTags.nix
@@ -1,5 +1,4 @@
 { bionix
-, nixpkgs
 , blacklist ? null
 , bwaIndexAttrs ? {}
 , faidxAttrs ? {}
@@ -8,9 +7,9 @@
 , heapSize ? "1G"
 }:
 
-with nixpkgs;
+with bionix;
 with lib;
-with bionix.types;
+with types;
 
 input:
 
@@ -21,9 +20,9 @@ in
 
 assert(sorted);
 
-stdenv.mkDerivation rec {
+stage rec {
   name = "gridss-computeSamTags";
-  buildInputs = [ jre ];
+  buildInputs = with pkgs; [ jre ];
   buildCommand = ''
     ln -s ${ref} ref.fa
     ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai
diff --git a/tools/gridss-configFile.nix b/tools/gridss-configFile.nix
index 15eba55..d6b600e 100644
--- a/tools/gridss-configFile.nix
+++ b/tools/gridss-configFile.nix
@@ -1,14 +1,15 @@
-{bionix, nixpkgs}:
+{bionix}:
 
-with nixpkgs;
+with bionix;
+with lib;
 
 let
     attrsToGridssConfigString = attrsToGridssConfigStringPrepend "";
 
     attrsToGridssConfigStringPrepend = prepend: attrs:
-        lib.concatStringsSep "\n" (
-            lib.attrValues (
-                lib.mapAttrs
+        concatStringsSep "\n" (
+            attrValues (
+                mapAttrs
                     (name: attr: prepend + (iniLine name attr))
                     attrs));
 
@@ -31,6 +32,6 @@ let
         # Allows for repeated fields (e.g. for adapters):
         list   = name: attr: concatStringsSep "\n" (map (x: iniLine name x) attr);
     };
-in configAttrs: (writeText
+in configAttrs: (pkgs.writeText
         "gridss.properties.override"
         ((attrsToGridssConfigString configAttrs) + "\n"))
diff --git a/tools/gridss-extractSVReads.nix b/tools/gridss-extractSVReads.nix
index 5fc4c59..f2fab30 100644
--- a/tools/gridss-extractSVReads.nix
+++ b/tools/gridss-extractSVReads.nix
@@ -1,5 +1,4 @@
 { bionix
-, nixpkgs
 , dictIndexAttrs ? {}
 , faidxAttrs ? {}
 , flags ? null
@@ -9,9 +8,9 @@
 , config ? null
 }:
 
-with nixpkgs;
+with bionix;
 with lib;
-with bionix.types;
+with types;
 
 input:
 
@@ -20,9 +19,9 @@ let
 in
 
 
-stdenv.mkDerivation rec {
+stage rec {
   name = "gridss-extractSVReads";
-  buildInputs = [ jre R ];
+  buildInputs = with pk