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-rwxr-xr-xlib/references.nix46
-rw-r--r--lib/types.nix6
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";