diff options
Diffstat (limited to 'lib')
| -rwxr-xr-x | lib/references.nix | 4 |
1 files changed, 2 insertions, 2 deletions
diff --git a/lib/references.nix b/lib/references.nix index 6675ac4..143c17a 100755 --- a/lib/references.nix +++ b/lib/references.nix @@ -31,7 +31,7 @@ rec { url = "ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/common_all_20180418.vcf.gz"; sha256 = "0r6m2yrcfw8bbdca515axjls30ssjas6x3qwi5qz07l3prjwmdd4"; }; - buildInputs = [ gawk ]; + buildInputs = with pkgs; [ gawk ]; buildCommand = '' gunzip < $src | awk '/^[^#]/{print "chr" $0;next}{print}' > $out ''; @@ -39,7 +39,7 @@ rec { }; cosmic = {coding, noncoding}: stage rec { name = "cosmic-grch38"; - buildInputs = [ gawk ]; + buildInputs = with pkgs; [ gawk ]; buildCommand = '' gunzip < ${coding} | grep '^#' > $out cat ${coding} ${noncoding} | gunzip | grep -v '^#' | sed 's/^/chr/' | sort -t$'\t' -k1,1 -k2,2n >> $out |