add encode blacklist to references

1 files changed, 105 insertions, 43 deletions

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
+      '';
     };
   };
 }