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authorJustin Bedo <cu@cua0.org>2019-02-15 15:06:40 +1100
committerJustin Bedo <cu@cua0.org>2019-02-15 15:06:40 +1100
commitf827a0142fc2e0f95deb18bc18ed372e444471e2 (patch)
tree868953651e00ba3a9f31c8bb9a8ee058dba3a11f /lib
parentbb7d6dce2f5f9ad4ebc39a80eff9e4cf66b34a28 (diff)
ref: missing pkg scope on gawk
Diffstat (limited to 'lib')
-rwxr-xr-xlib/references.nix4
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