From e4e46adf874a47a726f3f142c656ecaff9ee6cd3 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 18 Nov 2020 14:13:26 +1100
Subject: add encode blacklist to references
---
lib/references.nix | 148 +++++++++++++++++++++++++++++++++++++----------------
1 file changed, 105 insertions(+), 43 deletions(-)
(limited to 'lib')
diff --git a/lib/references.nix b/lib/references.nix
index 333888c..7b679be 100644
--- a/lib/references.nix
+++ b/lib/references.nix
@@ -9,38 +9,56 @@ 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";
+ 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 {};
+ passthru.filetype = filetype.fa { };
};
dbsnp = stage {
name = "dbsnp-b151_GRCh37p13";
src = pkgs.fetchurl {
- url = "ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/VCF/common_all_20180423.vcf.gz";
+ url =
+ "ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/VCF/common_all_20180423.vcf.gz";
sha256 = "0jf71h5wy82xhgsjkvp05mj2grjrjlnswmr0wz4lb87g3ip3c2mm";
};
buildInputs = with pkgs; [ gawk ];
buildCommand = ''
- gunzip < $src | awk '/^[^#]/{print "chr" $0;next}{print}' > $out
- '';
- passthru.filetype = filetype.vcf { ref = seq; };
+ gunzip < $src | awk '/^[^#]/{print "chr" $0;next}{print}' > $out
+ '';
+ passthru.filetype = filetype.vcf { ref = seq; };
+ };
+ encode.blacklist = stage {
+ # ENCSR636HFF
+ name = "blacklist";
+ bed = pkgs.fetchurl {
+ url =
+ "https://www.encodeproject.org/files/ENCFF001TDO/@@download/ENCFF001TDO.bed.gz";
+ sha256 = "168jiaiq4wdic7krxcdlfbm6jyxwk0l4w0c2yj6aq4lb9xzh0lq3";
};
- ensembl = let version = "74"; in {
+ buildCommand = ''
+ gunzip < $bed | awk '{print $1 ":" $2 "-" $3}' > $out
+ '';
+ };
+
+ ensembl = let version = "74";
+ in {
cdna = stage {
name = "ensembl-grch37-cdna-${version}";
src = pkgs.fetchurl {
- url = "ftp://ftp.ensembl.org/pub/release-${version}/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh37.${version}.cdna.all.fa.gz";
+ 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 > $out";
- passthru.filetype = filetype.fa {};
+ passthru.filetype = filetype.fa { };
};
gtf = stage {
name = "ensembl-grch37-gtf-${version}";
src = pkgs.fetchurl {
- url = "ftp://ftp.ensembl.org/pub/release-${version}/gtf/homo_sapiens/Homo_sapiens.GRCh37.${version}.gtf.gz";
+ url =
+ "ftp://ftp.ensembl.org/pub/release-${version}/gtf/homo_sapiens/Homo_sapiens.GRCh37.${version}.gtf.gz";
sha256 = "1m62hiw17zcxg3sza0aq53885wb8g202j8lc1ilhmkg2izzbyihj";
};
buildCommand = "gunzip < $src > $out";
@@ -50,7 +68,8 @@ rec {
db = pkgs.stdenv.mkDerivation rec {
name = "GRCh37.75";
src = pkgs.fetchurl {
- url = "mirror://sourceforge/project/snpeff/databases/v4_3/snpEff_v4_3_${name}.zip";
+ url =
+ "mirror://sourceforge/project/snpeff/databases/v4_3/snpEff_v4_3_${name}.zip";
sha256 = "19c8wwx91vq47z7j7f455vsv8jw067x5rd7449d1z0nln82zpmhm";
};
buildInputs = with pkgs; [ unzip ];
@@ -61,11 +80,13 @@ rec {
};
dbnsfp = {
db = fetchgdrive {
- url = "https://drive.google.com/uc?export=download&id=0B7Ms5xMSFMYlSTY5dDJjcHVRZ3M";
+ url =
+ "https://drive.google.com/uc?export=download&id=0B7Ms5xMSFMYlSTY5dDJjcHVRZ3M";
sha256 = "0gfzbid3pc10zds7ya50w4qfynsxgpyh7dx35vhm5f3h64mw75pm";
};
index = fetchgdrive {
- url = "https://drive.google.com/uc?export=download&id=0B7Ms5xMSFMYlOTV5RllpRjNHU2s";
+ url =
+ "https://drive.google.com/uc?export=download&id=0B7Ms5xMSFMYlOTV5RllpRjNHU2s";
sha256 = "0bwwigbnz32mmc8bczidjf68vv8x8i28zwkl2kgcbpj542zk5q86";
};
};
@@ -76,47 +97,65 @@ rec {
name = "seq-grch38.${version}";
version = "31";
src = pkgs.fetchurl {
- url = "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_${version}/GRCh38.p12.genome.fa.gz";
+ url =
+ "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_${version}/GRCh38.p12.genome.fa.gz";
sha256 = "1cmpg634likx3gbwn578491jjb8k7xm3cmqaqs3r9hyd195vbw98";
};
buildCommand = "gunzip < $src > $out";
- passthru.filetype = filetype.fa {};
+ passthru.filetype = filetype.fa { };
};
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";
+ url =
+ "ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/common_all_20180418.vcf.gz";
sha256 = "0r6m2yrcfw8bbdca515axjls30ssjas6x3qwi5qz07l3prjwmdd4";
};
buildInputs = with pkgs; [ gawk ];
buildCommand = ''
- gunzip < $src | awk '/^[^#]/{print "chr" $0;next}{print}' > $out
- '';
- passthru.filetype = filetype.vcf { ref = seq; };
+ gunzip < $src | awk '/^[^#]/{print "chr" $0;next}{print}' > $out
+ '';
+ passthru.filetype = filetype.vcf { ref = seq; };
+ };
+ encode.blacklist = stage {
+ # ENCSR636HFF
+ name = "blacklist";
+ bed = pkgs.fetchurl {
+ url =
+ "https://www.encodeproject.org/files/ENCFF356LFX/@@download/ENCFF356LFX.bed.gz";
+ sha256 = "sha256-qdCGzpDKZ/kzsprfv/Vup2i7zi7EsNUeLUBeWh1hu1Y=";
};
- ensembl = let version = "97"; in {
+ buildCommand = ''
+ gunzip < $bed | awk '{print $1 ":" $2 "-" $3}' > $out
+ '';
+ };
+ ensembl = let version = "97";
+ in {
cdna = stage {
name = "ensembl-grch38-cdna-${version}";
src = pkgs.fetchurl {
- url = "ftp://ftp.ensembl.org/pub/release-${version}/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz";
+ url =
+ "ftp://ftp.ensembl.org/pub/release-${version}/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz";
sha256 = "1m6hvnvlrsi6bzcmq0lnv0igy3in1a7jp723yc74g4g6zjp3cy8c";
};
buildCommand = "gunzip < $src > $out";
- passthru.filetype = filetype.fa {};
+ passthru.filetype = filetype.fa { };
};
ncrna = stage {
name = "ensembl-grch38-ncrna-${version}";
src = pkgs.fetchurl {
- url = "ftp://ftp.ensembl.org/pub/release-${version}/fasta/homo_sapiens/ncrna/Homo_sapiens.GRCh38.ncrna.fa.gz";
+ url =
+ "ftp://ftp.ensembl.org/pub/release-${version}/fasta/homo_sapiens/ncrna/Homo_sapiens.GRCh38.ncrna.fa.gz";
sha256 = "1r0dmybn31wf6xc90z2c08ngivkv39hqa8wqg3vik6s4spwpdhj0";
};
buildCommand = "gunzip < $src > $out";
- passthru.filetype = filetype.fa {};
+ passthru.filetype = filetype.fa { };
};
gtf = stage {
name = "ensembl-grch38-gtf-${version}";
src = pkgs.fetchurl {
- url = "ftp://ftp.ensembl.org/pub/release-${version}/gtf/homo_sapiens/Homo_sapiens.GRCh38.${version}.gtf.gz";
+ url =
+ "ftp://ftp.ensembl.org/pub/release-${version}/gtf/homo_sapiens/Homo_sapiens.GRCh38.${version}.gtf.gz";
sha256 = "068ab5jf87il301jcr0576c4q0smv6kxpv94gnrm3qzl6kvmaawd";
};
buildCommand = "gunzip < $src > $out";
@@ -124,7 +163,8 @@ rec {
gff3 = stage {
name = "ensembl-grch38-gff-${version}";
src = pkgs.fetchurl {
- url = "ftp://ftp.ensembl.org/pub/release-${version}/gff3/homo_sapiens/Homo_sapiens.GRCh38.${version}.gff3.gz";
+ url =
+ "ftp://ftp.ensembl.org/pub/release-${version}/gff3/homo_sapiens/Homo_sapiens.GRCh38.${version}.gff3.gz";
sha256 = "1xvhsn938mw0032qgc9dvw3k2xrhpx77b8ms03fkrs2s67f7zli7";
};
buildCommand = "gunzip < $src > $out";
@@ -134,7 +174,8 @@ rec {
db = pkgs.stdenv.mkDerivation rec {
name = "GRCh38.86";
src = pkgs.fetchurl {
- url = "mirror://sourceforge/project/snpeff/databases/v4_3/snpEff_v4_3_${name}.zip";
+ url =
+ "mirror://sourceforge/project/snpeff/databases/v4_3/snpEff_v4_3_${name}.zip";
sha256 = "1rf8q7l732ayjq2lpny4s75zpij05j00151374nqblk4wri2mz0i";
};
buildInputs = with pkgs; [ unzip ];
@@ -145,11 +186,13 @@ rec {
};
dbnsfp = {
db = fetchgdrive {
- url = "https://drive.google.com/uc?export=download&id=0B7Ms5xMSFMYlbTZodjlGUDZnTGc";
+ url =
+ "https://drive.google.com/uc?export=download&id=0B7Ms5xMSFMYlbTZodjlGUDZnTGc";
sha256 = "0gahnwkc7v2q6p6ixkhvsgqvvm6xf0c3bdh4nf0alih83h3wffd0";
};
index = fetchgdrive {
- url = "https://drive.google.com/uc?export=download&id=0B7Ms5xMSFMYlNVBJdFA5cFZRYkE";
+ url =
+ "https://drive.google.com/uc?export=download&id=0B7Ms5xMSFMYlNVBJdFA5cFZRYkE";
sha256 = "18blkly6gvg7r0sx968xlb1zl2kqg5j1kpbrm2r7ajlxlfyvrx3w";
};
};
@@ -157,7 +200,8 @@ rec {
UCSCgenes = stage {
name = "UCSCgenes";
src = pkgs.fetchurl {
- url = "http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refFlat.txt.gz";
+ url =
+ "http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refFlat.txt.gz";
sha256 = "1f53myn4vpvswzssx2xsiq9si8w58gpcm0f32srq220w36hq9md4";
};
buildCommand = "gunzip < $src > $out";
@@ -170,38 +214,41 @@ rec {
name = "seq-grcm38.${version}";
version = "p6";
src = pkgs.fetchurl {
- url = "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M19/GRCm38.${version}.genome.fa.gz";
+ url =
+ "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M19/GRCm38.${version}.genome.fa.gz";
sha256 = "0ryiqab5bldpzawylsk2qpjxr2j701q03ww9jqyxhkimqpn9g3mr";
};
buildCommand = "gunzip < $src > $out";
- passthru.filetype = filetype.fa {};
+ passthru.filetype = filetype.fa { };
};
- ensembl = let
- version = "94";
+ ensembl = let version = "94";
in {
cdna = stage {
name = "ensembl-grcm38-cdna-${version}";
src = pkgs.fetchurl {
- url = "ftp://ftp.ensembl.org/pub/release-${version}/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz";
+ url =
+ "ftp://ftp.ensembl.org/pub/release-${version}/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz";
sha256 = "0khp9l6s35lav2xqp7vkk6ybnz4wjihn7lapjf2lbpnbzjb4hp6d";
};
buildCommand = "gunzip < $src > $out";
- passthru.filetype = filetype.fa {};
+ passthru.filetype = filetype.fa { };
};
ncrna = stage {
name = "ensembl-grcm38-ncrna-${version}";
version = "94";
src = pkgs.fetchurl {
- url = "ftp://ftp.ensembl.org/pub/release-${version}/fasta/mus_musculus/ncrna/Mus_musculus.GRCm38.ncrna.fa.gz";
+ url =
+ "ftp://ftp.ensembl.org/pub/release-${version}/fasta/mus_musculus/ncrna/Mus_musculus.GRCm38.ncrna.fa.gz";
sha256 = "0d997gm8p2b89rm5d46m2x4vz9lijxarfr2lzylnbi8gyqrbagdd";
};
buildCommand = "gunzip < $src > $out";
- passthru.filetype = filetype.fa {};
+ passthru.filetype = filetype.fa { };
};
gtf = stage {
name = "ensembl-grcm38-gtf-${version}";
src = pkgs.fetchurl {
- url = "ftp://ftp.ensembl.org/pub/release-${version}/gtf/mus_musculus/Mus_musculus.GRCm38.${version}.gtf.gz";
+ url =
+ "ftp://ftp.ensembl.org/pub/release-${version}/gtf/mus_musculus/Mus_musculus.GRCm38.${version}.gtf.gz";
sha256 = "0i61jq5i5bcini5nxqxxp3rnz2xzgychvzdn0k451f5rv053lp3v";
};
buildCommand = "gunzip < $src > $out";
@@ -209,7 +256,8 @@ rec {
gff3 = stage {
name = "ensembl-grcm38-gff-${version}";
src = pkgs.fetchurl {
- url = "ftp://ftp.ensembl.org/pub/release-${version}/gff3/mus_musculus/Mus_musculus.GRCm38.${version}.gff3.gz";
+ url =
+ "ftp://ftp.ensembl.org/pub/release-${version}/gff3/mus_musculus/Mus_musculus.GRCm38.${version}.gff3.gz";
sha256 = "15fmdpx6g96fygwhs10jwrb2q5p9y64bc3d4clg856k57qzzgprg";
};
buildCommand = "gunzip < $src > $out";
@@ -223,11 +271,25 @@ rec {
name = "seq-mm10.${version}";
version = "p4";
src = pkgs.fetchurl {
- url = "http://hgdownload.soe.ucsc.edu/goldenPath/mm10/mm10Patch4/mm10Patch4.fa.gz";
- sha256 = "1660d6d05f3aa266c6053cfd1efef1747d9e854836917241d6f47cff7a55340c";
+ url =
+ "http://hgdownload.soe.ucsc.edu/goldenPath/mm10/mm10Patch4/mm10Patch4.fa.gz";
+ sha256 =
+ "1660d6d05f3aa266c6053cfd1efef1747d9e854836917241d6f47cff7a55340c";
};
buildCommand = "gunzip < $src > $out";
- passthru.filetype = filetype.fa {};
+ passthru.filetype = filetype.fa { };
+ };
+ encode.blacklist = stage {
+ # ENCSR636HFF
+ name = "blacklist";
+ bed = pkgs.fetchurl {
+ url =
+ "https://www.encodeproject.org/files/ENCFF547MET/@@download/ENCFF547MET.bed.gz";
+ sha256 = "sha256-jMihs76hdBAw6RRHhdY91YrLOfctcaxHKYwLeDKKysk=";
+ };
+ buildCommand = ''
+ gunzip < $bed | awk '{print $1 ":" $2 "-" $3}' > $out
+ '';
};
};
}
--
cgit v1.2.3