diff options
author | Justin Bedo <cu@cua0.org> | 2019-01-23 09:02:13 +1100 |
---|---|---|
committer | Justin Bedo <cu@cua0.org> | 2019-01-23 09:02:13 +1100 |
commit | 71a9142f58f0e9e738ca1450b91b4672ed41521d (patch) | |
tree | ec0d67ba436183332f2c30dbedd507ab602fa8f1 /lib | |
parent | 61c558f76638f51518b08b12188c40abdcf5e31c (diff) |
stage: change to stdenvNoCC
Diffstat (limited to 'lib')
-rwxr-xr-x | lib/references.nix | 24 |
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 { |