diff options
author | Justin Bedo <cu@cua0.org> | 2019-09-25 10:15:50 +1000 |
---|---|---|
committer | Justin Bedo <cu@cua0.org> | 2019-09-25 10:15:50 +1000 |
commit | 98f0ae6573ce16caac006c2da70f0beb65cb2696 (patch) | |
tree | 7926a98df7eef84b77b6685dfda81c13d83eb179 | |
parent | db5679e3ad4e343dd710dad474169a30cff68eb9 (diff) |
add grch37
-rw-r--r-- | lib/references.nix | 61 |
1 files changed, 59 insertions, 2 deletions
diff --git a/lib/references.nix b/lib/references.nix index a55637f..157ba8d 100644 --- a/lib/references.nix +++ b/lib/references.nix @@ -4,13 +4,70 @@ with bionix; with types; rec { + grch37 = rec { + seq = stage rec { + name = "seq-grch37.${version}"; + version = "19"; + src = pkgs.fetchurl { + url = "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_${version}/GRCh37.p13.genome.fa.gz"; + sha256 = "1midmq3kaci3nizg37nqzv9syfasimgxxvg8az8gz0fi1ksljw53"; + }; + buildCommand = "gunzip < $src > $out"; + passthru.filetype = filetype.fa {}; + }; + ensembl = let version = "74"; in { + cdna = stage { + name = "ensembl-grch37-cdna-${version}"; + src = pkgs.fetchurl { + url = "ftp://ftp.ensembl.org/pub/release-${version}/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh37.${version}.cdna.all.fa.gz"; + sha256 = "1m62hiw17zcxg3sza0aq53885wb8g202j8lc1ilhmkg2izzbyihj"; + }; + buildCommand = "gunzip < $src > $out"; + passthru.filetype = filetype.fa {}; + }; + gtf = stage { + name = "ensembl-grch37-gtf-${version}"; + src = pkgs.fetchurl { + url = "ftp://ftp.ensembl.org/pub/release-${version}/gtf/homo_sapiens/Homo_sapiens.GRCh37.${version}.gtf.gz"; + sha256 = "1m62hiw17zcxg3sza0aq53885wb8g202j8lc1ilhmkg2izzbyihj"; + }; + buildCommand = "gunzip < $src > $out"; + }; + }; + snpeff = { + db = pkgs.stdenv.mkDerivation rec { + name = "GRCh37.87"; + src = pkgs.fetchurl { + url = "mirror://sourceforge/project/snpeff/databases/v4_3/snpEff_v4_3_${name}.zip"; + sha256 = "0ybbj4470ilc4csmgfjqd6hqq4krwjws97ywjnqrhbi4dcq3h3bg"; + }; + buildInputs = with pkgs; [ unzip ]; + buildCommand = '' + unzip ${src} + mv data/${name} $out + ''; + }; + dbnsfp = { + db = pkgs.requireFile { + name = "dbNSFP.txt.gz"; + message = "download the dbNSFP database manually from https://drive.google.com/uc?export=download&id=0B7Ms5xMSFMYlSTY5dDJjcHVRZ3M and add to nix store"; + sha256 = "0gfzbid3pc10zds7ya50w4qfynsxgpyh7dx35vhm5f3h64mw75pm"; + }; + index = pkgs.requireFile { + name = "dbNSFP.txt.gz.tbi"; + message = "download the dbNSFP index manually from https://drive.google.com/uc?export=download&id=0B7Ms5xMSFMYlOTV5RllpRjNHU2s and add to nix store"; + sha256 = "0bwwigbnz32mmc8bczidjf68vv8x8i28zwkl2kgcbpj542zk5q86"; + }; + }; + }; + }; grch38 = grch38-p12; grch38-p12 = rec { seq = stage rec { name = "seq-grch38.${version}"; - version = "p12"; + version = "32"; src = pkgs.fetchurl { - url = "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_28/GRCh38.p12.genome.fa.gz"; + url = "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_${version}/GRCh38.p13.genome.fa.gz"; sha256 = "0ji2ggpmgnbpwbhq8mirj6h3lyy02nl2rnz7n892iq5cqpsblh4z"; }; buildCommand = "gunzip < $src > $out"; |