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-rw-r--r--lib/references.nix265
1 files changed, 123 insertions, 142 deletions
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 {};
+ };
+ };
+}
generated by cgit v1.2.3 (git 2.25.1) at 2024-12-26 05:26:06 +0000