blob: a55637f9f08f7eb51163c1c0a26b332465177e3e (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
|
{ bionix }:
with bionix;
with types;
rec {
grch38 = grch38-p12;
grch38-p12 = rec {
seq = stage rec {
name = "seq-grch38.${version}";
version = "p12";
src = pkgs.fetchurl {
url = "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_28/GRCh38.p12.genome.fa.gz";
sha256 = "0ji2ggpmgnbpwbhq8mirj6h3lyy02nl2rnz7n892iq5cqpsblh4z";
};
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 {
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; };
};
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 >> $out
'';
passthru.filetype = filetype.vcf { ref = seq; };
};
ensembl = let version = "94"; in {
cdna = stage {
name = "ensembl-grch38-cdna-${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";
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";
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.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 > $out";
};
};
};
mm10 = mm10-p4;
mm10-p4 = {
seq = stage rec {
name = "seq-mm10.${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 {};
};
};
}
|
