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-rwxr-xr-xlib/references.nix24
1 files changed, 12 insertions, 12 deletions
diff --git a/lib/references.nix b/lib/references.nix
index 11a0eea..ebd61fc 100755
--- a/lib/references.nix
+++ b/lib/references.nix
@@ -6,7 +6,7 @@ with types;
rec {
grch38 = grch38-p12;
grch38-p12 = rec {
- seq = pkgs.stdenvNoCC.mkDerivation rec {
+ seq = stage rec {
name = "seq-grch38.${version}";
version = "p12";
src = pkgs.fetchurl {
@@ -16,7 +16,7 @@ rec {
buildCommand = "gunzip < $src > $out";
passthru.filetype = filetype.fa {};
};
- blacklist = pkgs.stdenvNoCC.mkDerivation {
+ blacklist = stage {
name = "blacklist-grch38";
src = pkgs.fetchurl {
url = "http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38-human/hg38.blacklist.bed.gz";
@@ -25,7 +25,7 @@ rec {
buildCommand = "gunzip < $src > $out";
passthru.filetype = filetype.bed { ref = seq; };
};
- dbsnp = pkgs.stdenvNoCC.mkDerivation {
+ dbsnp = stage {
name = "dbsnp-b151_GRCh38p7";
src = pkgs.fetchurl {
url = "ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/common_all_20180418.vcf.gz";
@@ -37,7 +37,7 @@ rec {
'';
passthru.filetype = filetype.vcf { ref = seq; };
};
- cosmic = {coding, noncoding}: pkgs.stdenvNoCC.mkDerivation rec {
+ cosmic = {coding, noncoding}: stage rec {
name = "cosmic-grch38";
buildInputs = [ gawk ];
buildCommand = ''
@@ -47,7 +47,7 @@ rec {
passthru.filetype = filetype.vcf { ref = seq; };
};
ensembl = {
- cdna = pkgs.stdenvNoCC.mkDerivation rec {
+ cdna = stage rec {
name = "ensembl-grch38-cdna-${version}";
version = "94";
src = pkgs.fetchurl {
@@ -57,7 +57,7 @@ rec {
buildCommand = "gunzip < $src > $out";
passthru.filetype = filetype.fa {};
};
- ncrna = pkgs.stdenvNoCC.mkDerivation rec {
+ ncrna = stage rec {
name = "ensembl-grch38-ncrna-${version}";
version = "94";
src = pkgs.fetchurl {
@@ -82,12 +82,12 @@ rec {
'';
};
dbnsfp = {
- db = requireFile {
+ db = pkgs.requireFile {
name = "dbNSFP.txt.gz";
message = "download the dbNSFP database manually from https://drive.google.com/uc?export=download&id=0B7Ms5xMSFMYlbTZodjlGUDZnTGc and add to nix store";
sha256 = "0gahnwkc7v2q6p6ixkhvsgqvvm6xf0c3bdh4nf0alih83h3wffd0";
};
- index = requireFile {
+ index = pkgs.requireFile {
name = "dbNSFP.txt.gz.tbi";
message = "download the dbNSFP index manually from https://drive.google.com/uc?export=download&id=0B7Ms5xMSFMYlNVBJdFA5cFZRYkE and add to nix store";
sha256 = "18blkly6gvg7r0sx968xlb1zl2kqg5j1kpbrm2r7ajlxlfyvrx3w";
@@ -106,7 +106,7 @@ rec {
grcm38 = grcm38-p6;
grcm38-p6 = {
- seq = pkgs.stdenvNoCC.mkDerivation rec {
+ seq = stage rec {
name = "seq-grcm38.${version}";
version = "p6";
src = pkgs.fetchurl {
@@ -117,7 +117,7 @@ rec {
passthru.filetype = filetype.fa {};
};
ensembl = {
- cdna = pkgs.stdenvNoCC.mkDerivation rec {
+ cdna = stage rec {
name = "ensembl-grch38-cdna-${version}";
version = "94";
src = pkgs.fetchurl {
@@ -127,7 +127,7 @@ rec {
buildCommand = "gunzip < $src > $out";
passthru.filetype = filetype.fa {};
};
- ncrna = pkgs.stdenvNoCC.mkDerivation rec {
+ ncrna = stage rec {
name = "ensembl-grch38-ncrna-${version}";
version = "94";
src = pkgs.fetchurl {
@@ -142,7 +142,7 @@ rec {
mm10 = mm10-p4;
mm10-p4 = {
- seq = pkgs.stdenvNoCC.mkDerivation rec {
+ seq = stage rec {
name = "seq-mm10.${version}";
version = "p4";
src = pkgs.fetchurl {