diff options
author | Justin Bedo <cu@cua0.org> | 2021-10-29 17:39:01 +1100 |
---|---|---|
committer | Justin Bedo <cu@cua0.org> | 2021-10-29 17:39:01 +1100 |
commit | bac9248a5e08e8afdf5485a6e27cfe72e1ca5090 (patch) | |
tree | 8719a280b56122017d46b582cd3da8547dd3f548 /lib/references.nix | |
parent | ab809b8c77efdad9fb54d3591a0193a1cbe888d1 (diff) |
treewide reformatting and simplification
- simplify with statix
- reformat with nixpkgs-fmt
Diffstat (limited to 'lib/references.nix')
-rw-r--r-- | lib/references.nix | 194 |
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; |