From d5cca20453498dbabb04a91f4abe856cb4a6bb6d Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 25 Sep 2019 11:26:58 +1000
Subject: =?UTF-8?q?grch38.31=20=E2=86=92=20grch38.32?=
MIME-Version: 1.0
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---
 lib/references.nix | 265 +++++++++++++++++++++++++----------------------------
 1 file changed, 123 insertions(+), 142 deletions(-)

(limited to 'lib')

diff --git a/lib/references.nix b/lib/references.nix
index 157ba8d..7f754d6 100644
--- a/lib/references.nix
+++ b/lib/references.nix
@@ -61,27 +61,17 @@ rec {
       };
     };
   };
-  grch38 = grch38-p12;
-  grch38-p12 = rec {
+  grch38 = rec {
     seq = stage rec {
       name = "seq-grch38.${version}";
-      version = "32";
+      version = "31";
       src = pkgs.fetchurl {
-        url = "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_${version}/GRCh38.p13.genome.fa.gz";
-        sha256 = "0ji2ggpmgnbpwbhq8mirj6h3lyy02nl2rnz7n892iq5cqpsblh4z";
+        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 {};
     };
-    blacklist = stage {
-      name = "blacklist-grch38";
-      src = pkgs.fetchurl {
-        url = "http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38-human/hg38.blacklist.bed.gz";
-        sha256 = "1lpnqq1mjidbdxj5i6x26rxa8x1rs8q3hlf0z1z49j3jsnkgffky";
-      };
-      buildCommand = "gunzip < $src > $out";
-      passthru.filetype = filetype.bed { ref = seq; };
-    };
     dbsnp = stage {
       name = "dbsnp-b151_GRCh38p7";
       src = pkgs.fetchurl {
@@ -94,151 +84,142 @@ rec {
         '';
         passthru.filetype = filetype.vcf { ref = seq; };
       };
-      cosmic = {coding, noncoding}: stage rec {
-        name = "cosmic-grch38";
-        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 >> $out
-        '';
-        passthru.filetype = filetype.vcf { ref = seq; };
+    ensembl = let version = "97"; in {
+      cdna = stage {
+        name = "ensembl-grch38-cdna-${version}";
+        src = pkgs.fetchurl {
+          url = "ftp://ftp.ensembl.org/pub/release-${version}/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz";
+          sha256 = "1m6hvnvlrsi6bzcmq0lnv0igy3in1a7jp723yc74g4g6zjp3cy8c";
+        };
+        buildCommand = "gunzip < $src > $out";
+        passthru.filetype = filetype.fa {};
       };
-      ensembl = let version = "94"; in {
-        cdna = stage {
-          name = "ensembl-grch38-cdna-${version}";
-          src = pkgs.fetchurl {
-            url = "ftp://ftp.ensembl.org/pub/release-${version}/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz";
-            sha256 = "1fc5d6p2wlwsm49wnmxmm3byjx5jvr6z9fpzrq7v7fpb086adl0h";
-          };
-          buildCommand = "gunzip < $src > $out";
-          passthru.filetype = filetype.fa {};
-        };
-        ncrna = stage {
-          name = "ensembl-grch38-ncrna-${version}";
-          src = pkgs.fetchurl {
-            url = "ftp://ftp.ensembl.org/pub/release-${version}/fasta/homo_sapiens/ncrna/Homo_sapiens.GRCh38.ncrna.fa.gz";
-            sha256 = "1cpasykwriila52nqgvw6d3mjyh6d9qi613hvhn4h1dxkqzgnjff";
-          };
-          buildCommand = "gunzip < $src > $out";
-          passthru.filetype = filetype.fa {};
-        };
-        gtf = stage {
-          name = "ensembl-grch38-gtf-${version}";
-          src = pkgs.fetchurl {
-            url = "ftp://ftp.ensembl.org/pub/release-${version}/gtf/homo_sapiens/Homo_sapiens.GRCh38.${version}.gtf.gz";
-            sha256 = "124swjp6bhhl0wjhfq16675s3fqyny293mhrjwvzkiybpgfwzpi7";
-          };
-          buildCommand = "gunzip < $src > $out";
-        };
-        gff3 = stage {
-          name = "ensembl-grch38-gff-${version}";
-          src = pkgs.fetchurl {
-            url = "ftp://ftp.ensembl.org/pub/release-${version}/gff3/homo_sapiens/Homo_sapiens.GRCh38.${version}.gff3.gz";
-            sha256 = "0r2npkpq7z0dd74fl8q3kzv0860chfx3v319z6libl5qy9rspdmi";
-          };
-          buildCommand = "gunzip < $src > $out";
-        };
-      };
-      snpeff = {
-        db = pkgs.stdenv.mkDerivation rec {
-          name = "GRCh38.86";
-          src = pkgs.fetchurl {
-            url = "mirror://sourceforge/project/snpeff/databases/v4_3/snpEff_v4_3_${name}.zip";
-            sha256 = "1rf8q7l732ayjq2lpny4s75zpij05j00151374nqblk4wri2mz0i";
-          };
-          buildInputs = with pkgs; [ unzip ];
-          buildCommand = ''
-            unzip ${src}
-            mv data/${name} $out
-          '';
-        };
-        dbnsfp = {
-          db = pkgs.requireFile {
-            name = "dbNSFP.txt.gz";
-            message = "download the dbNSFP database manually from https://drive.google.com/uc?export=download&id=0B7Ms5xMSFMYlbTZodjlGUDZnTGc and add to nix store";
-            sha256 = "0gahnwkc7v2q6p6ixkhvsgqvvm6xf0c3bdh4nf0alih83h3wffd0";
-          };
-          index = pkgs.requireFile {
-            name = "dbNSFP.txt.gz.tbi";
-            message = "download the dbNSFP index manually from https://drive.google.com/uc?export=download&id=0B7Ms5xMSFMYlNVBJdFA5cFZRYkE and add to nix store";
-            sha256 = "18blkly6gvg7r0sx968xlb1zl2kqg5j1kpbrm2r7ajlxlfyvrx3w";
-          };
-        };
-      };
-      UCSCgenes = stage {
-        name = "UCSCgenes";
+      ncrna = stage {
+        name = "ensembl-grch38-ncrna-${version}";
         src = pkgs.fetchurl {
-          url = "http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refFlat.txt.gz";
-          sha256 = "1f53myn4vpvswzssx2xsiq9si8w58gpcm0f32srq220w36hq9md4";
+          url = "ftp://ftp.ensembl.org/pub/release-${version}/fasta/homo_sapiens/ncrna/Homo_sapiens.GRCh38.ncrna.fa.gz";
+          sha256 = "1r0dmybn31wf6xc90z2c08ngivkv39hqa8wqg3vik6s4spwpdhj0";
         };
         buildCommand = "gunzip < $src > $out";
+        passthru.filetype = filetype.fa {};
+      };
+      gtf = stage {
+        name = "ensembl-grch38-gtf-${version}";
+        src = pkgs.fetchurl {
+          url = "ftp://ftp.ensembl.org/pub/release-${version}/gtf/homo_sapiens/Homo_sapiens.GRCh38.${version}.gtf.gz";
+          sha256 = "068ab5jf87il301jcr0576c4q0smv6kxpv94gnrm3qzl6kvmaawd";
+        };
+        buildCommand = "gunzip < $src > $out";
+      };
+      gff3 = stage {
+        name = "ensembl-grch38-gff-${version}";
+        src = pkgs.fetchurl {
+          url = "ftp://ftp.ensembl.org/pub/release-${version}/gff3/homo_sapiens/Homo_sapiens.GRCh38.${version}.gff3.gz";
+          sha256 = "1xvhsn938mw0032qgc9dvw3k2xrhpx77b8ms03fkrs2s67f7zli7";
+        };
+        buildCommand = "gunzip < $src > $out";
+      };
+    };
+    snpeff = {
+      db = pkgs.stdenv.mkDerivation rec {
+        name = "GRCh38.86";
+        src = pkgs.fetchurl {
+          url = "mirror://sourceforge/project/snpeff/databases/v4_3/snpEff_v4_3_${name}.zip";
+          sha256 = "1rf8q7l732ayjq2lpny4s75zpij05j00151374nqblk4wri2mz0i";
+        };
+        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=0B7Ms5xMSFMYlbTZodjlGUDZnTGc and add to nix store";
+          sha256 = "0gahnwkc7v2q6p6ixkhvsgqvvm6xf0c3bdh4nf0alih83h3wffd0";
+        };
+        index = pkgs.requireFile {
+          name = "dbNSFP.txt.gz.tbi";
+          message = "download the dbNSFP index manually from https://drive.google.com/uc?export=download&id=0B7Ms5xMSFMYlNVBJdFA5cFZRYkE and add to nix store";
+          sha256 = "18blkly6gvg7r0sx968xlb1zl2kqg5j1kpbrm2r7ajlxlfyvrx3w";
+        };
       };
     };
+    UCSCgenes = stage {
+      name = "UCSCgenes";
+      src = pkgs.fetchurl {
+        url = "http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refFlat.txt.gz";
+        sha256 = "1f53myn4vpvswzssx2xsiq9si8w58gpcm0f32srq220w36hq9md4";
+      };
+      buildCommand = "gunzip < $src > $out";
+    };
+  };
 
-    grcm38 = grcm38-p6;
-    grcm38-p6 = {
-      seq = stage rec {
-        name = "seq-grcm38.${version}";
-        version = "p6";
+  grcm38 = grcm38-p6;
+  grcm38-p6 = {
+    seq = stage rec {
+      name = "seq-grcm38.${version}";
+      version = "p6";
+      src = pkgs.fetchurl {
+        url = "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M19/GRCm38.${version}.genome.fa.gz";
+        sha256 = "0ryiqab5bldpzawylsk2qpjxr2j701q03ww9jqyxhkimqpn9g3mr";
+      };
+      buildCommand = "gunzip < $src > $out";
+      passthru.filetype = filetype.fa {};
+    };
+    ensembl = let
+      version = "94";
+    in {
+      cdna = stage {
+        name = "ensembl-grcm38-cdna-${version}";
         src = pkgs.fetchurl {
-          url = "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M19/GRCm38.${version}.genome.fa.gz";
-          sha256 = "0ryiqab5bldpzawylsk2qpjxr2j701q03ww9jqyxhkimqpn9g3mr";
+          url = "ftp://ftp.ensembl.org/pub/release-${version}/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz";
+          sha256 = "0khp9l6s35lav2xqp7vkk6ybnz4wjihn7lapjf2lbpnbzjb4hp6d";
         };
         buildCommand = "gunzip < $src > $out";
         passthru.filetype = filetype.fa {};
       };
-      ensembl = let
+      ncrna = stage {
+        name = "ensembl-grcm38-ncrna-${version}";
         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";
-            sha256 = "0khp9l6s35lav2xqp7vkk6ybnz4wjihn7lapjf2lbpnbzjb4hp6d";
-          };
-          buildCommand = "gunzip < $src > $out";
-          passthru.filetype = filetype.fa {};
-        };
-        ncrna = stage {
-          name = "ensembl-grcm38-ncrna-${version}";
-          version = "94";
-          src = pkgs.fetchurl {
-            url = "ftp://ftp.ensembl.org/pub/release-${version}/fasta/mus_musculus/ncrna/Mus_musculus.GRCm38.ncrna.fa.gz";
-            sha256 = "0d997gm8p2b89rm5d46m2x4vz9lijxarfr2lzylnbi8gyqrbagdd";
-          };
-          buildCommand = "gunzip < $src > $out";
-          passthru.filetype = filetype.fa {};
-        };
-        gtf = stage {
-          name = "ensembl-grcm38-gtf-${version}";
-          src = pkgs.fetchurl {
-            url = "ftp://ftp.ensembl.org/pub/release-${version}/gtf/mus_musculus/Mus_musculus.GRCm38.${version}.gtf.gz";
-            sha256 = "0i61jq5i5bcini5nxqxxp3rnz2xzgychvzdn0k451f5rv053lp3v";
-          };
-          buildCommand = "gunzip < $src > $out";
-        };
-        gff3 = stage {
-          name = "ensembl-grcm38-gff-${version}";
-          src = pkgs.fetchurl {
-            url = "ftp://ftp.ensembl.org/pub/release-${version}/gff3/mus_musculus/Mus_musculus.GRCm38.${version}.gff3.gz";
-            sha256 = "15fmdpx6g96fygwhs10jwrb2q5p9y64bc3d4clg856k57qzzgprg";
-          };
-          buildCommand = "gunzip < $src > $out";
+        src = pkgs.fetchurl {
+          url = "ftp://ftp.ensembl.org/pub/release-${version}/fasta/mus_musculus/ncrna/Mus_musculus.GRCm38.ncrna.fa.gz";
+          sha256 = "0d997gm8p2b89rm5d46m2x4vz9lijxarfr2lzylnbi8gyqrbagdd";
         };
+        buildCommand = "gunzip < $src > $out";
+        passthru.filetype = filetype.fa {};
       };
-    };
-
-    mm10 = mm10-p4;
-    mm10-p4 = {
-      seq = stage rec {
-        name = "seq-mm10.${version}";
-        version = "p4";
+      gtf = stage {
+        name = "ensembl-grcm38-gtf-${version}";
         src = pkgs.fetchurl {
-          url = "http://hgdownload.soe.ucsc.edu/goldenPath/mm10/mm10Patch4/mm10Patch4.fa.gz";
-          sha256 = "1660d6d05f3aa266c6053cfd1efef1747d9e854836917241d6f47cff7a55340c";
+          url = "ftp://ftp.ensembl.org/pub/release-${version}/gtf/mus_musculus/Mus_musculus.GRCm38.${version}.gtf.gz";
+          sha256 = "0i61jq5i5bcini5nxqxxp3rnz2xzgychvzdn0k451f5rv053lp3v";
+        };
+        buildCommand = "gunzip < $src > $out";
+      };
+      gff3 = stage {
+        name = "ensembl-grcm38-gff-${version}";
+        src = pkgs.fetchurl {
+          url = "ftp://ftp.ensembl.org/pub/release-${version}/gff3/mus_musculus/Mus_musculus.GRCm38.${version}.gff3.gz";
+          sha256 = "15fmdpx6g96fygwhs10jwrb2q5p9y64bc3d4clg856k57qzzgprg";
         };
         buildCommand = "gunzip < $src > $out";
-        passthru.filetype = filetype.fa {};
       };
     };
-  }
+  };
+
+  mm10 = mm10-p4;
+  mm10-p4 = {
+    seq = stage rec {
+      name = "seq-mm10.${version}";
+      version = "p4";
+      src = pkgs.fetchurl {
+        url = "http://hgdownload.soe.ucsc.edu/goldenPath/mm10/mm10Patch4/mm10Patch4.fa.gz";
+        sha256 = "1660d6d05f3aa266c6053cfd1efef1747d9e854836917241d6f47cff7a55340c";
+      };
+      buildCommand = "gunzip < $src > $out";
+      passthru.filetype = filetype.fa {};
+    };
+  };
+}
-- 
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