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-rw-r--r--lib/references.nix194
1 files changed, 100 insertions, 94 deletions
diff --git a/lib/references.nix b/lib/references.nix
index 23ccde3..fd8c3cc 100644
--- a/lib/references.nix
+++ b/lib/references.nix
@@ -26,7 +26,7 @@ rec {
buildInputs = with pkgs; [ gawk ];
buildCommand = ''
gunzip < $src | awk '/^[^#]/{print "chr" $0;next}{print}' > $out
- '';
+ '';
passthru.filetype = filetype.vcf { ref = seq; };
};
encode.blacklist = stage {
@@ -42,28 +42,30 @@ rec {
'';
};
- ensembl = let version = "74";
- in {
- cdna = stage {
- name = "ensembl-grch37-cdna-${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";
+ 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 { };
};
- 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";
+ 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";
};
- buildCommand = "gunzip < $src > $out";
};
- };
snpeff = {
db = pkgs.stdenv.mkDerivation rec {
name = "GRCh37.75";
@@ -114,7 +116,7 @@ rec {
buildInputs = with pkgs; [ gawk ];
buildCommand = ''
gunzip < $src | awk '/^[^#]/{print "chr" $0;next}{print}' > $out
- '';
+ '';
passthru.filetype = filetype.vcf { ref = seq; };
};
encode.blacklist = stage {
@@ -129,47 +131,49 @@ rec {
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-${version}/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz";
- sha256 = "1m6hvnvlrsi6bzcmq0lnv0igy3in1a7jp723yc74g4g6zjp3cy8c";
+ ensembl =
+ let version = "97";
+ in
+ {
+ cdna = stage {
+ name = "ensembl-grch38-cdna-${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 { };
};
- 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-${version}/fasta/homo_sapiens/ncrna/Homo_sapiens.GRCh38.ncrna.fa.gz";
- sha256 = "1r0dmybn31wf6xc90z2c08ngivkv39hqa8wqg3vik6s4spwpdhj0";
+ ncrna = stage {
+ name = "ensembl-grch38-ncrna-${version}";
+ src = pkgs.fetchurl {
+ url =
+ "ftp://ftp.ensembl.org/pub/release-${version}/fasta/homo_sapiens/ncrna/Homo_sapiens.GRCh38.ncrna.fa.gz";
+ sha256 = "1r0dmybn31wf6xc90z2c08ngivkv39hqa8wqg3vik6s4spwpdhj0";
+ };
+ buildCommand = "gunzip < $src > $out";
+ passthru.filetype = filetype.fa { };
};
- 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";
+ 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";
};
- 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";
+ 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";
};
- buildCommand = "gunzip < $src > $out";
};
- };
snpeff = {
db = pkgs.stdenv.mkDerivation rec {
name = "GRCh38.86";
@@ -221,48 +225,50 @@ rec {
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.ensembl.org/pub/release-${version}/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz";
- sha256 = "0khp9l6s35lav2xqp7vkk6ybnz4wjihn7lapjf2lbpnbzjb4hp6d";
+ ensembl =
+ let version = "94";
+ in
+ {
+ cdna = stage {
+ name = "ensembl-grcm38-cdna-${version}";
+ src = pkgs.fetchurl {
+ url =
+ "ftp://ftp.ensembl.org/pub/release-${version}/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz";
+ sha256 = "0khp9l6s35lav2xqp7vkk6ybnz4wjihn7lapjf2lbpnbzjb4hp6d";
+ };
+ buildCommand = "gunzip < $src > $out";
+ passthru.filetype = filetype.fa { };
};
- 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-${version}/fasta/mus_musculus/ncrna/Mus_musculus.GRCm38.ncrna.fa.gz";
- sha256 = "0d997gm8p2b89rm5d46m2x4vz9lijxarfr2lzylnbi8gyqrbagdd";
+ ncrna = stage {
+ name = "ensembl-grcm38-ncrna-${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 { };
};
- 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";
+ 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";
};
- 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";
+ 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";
};
- buildCommand = "gunzip < $src > $out";
};
- };
};
mm10 = mm10-p4;
generated by cgit v1.2.3 (git 2.25.1) at 2024-05-07 18:35:03 +0000