large refactor

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

2 files changed, 26 insertions, 26 deletions

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";