blob: 21403a2dfd69db49bb3596bf1ff08d1691446fd8 (
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
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
|
{ nixpkgs ? import <nixpkgs> { }, overlays ? [ ] }:
let
inherit (nixpkgs) fetchurl callPackage;
bionix = nixpkgs.lib.makeExtensible (self:
let callBionix = file: attrs: import file ({ bionix = self; } // attrs);
in
with self; {
inherit callBionix;
id = x: x;
exec = id;
exec' = f: exec (_: f) { };
exec'' = f: exec' (_: f) { };
callBionixE = p: exec (callBionix p);
types = callBionix ./lib/types.nix { };
fetchgdrive = callBionix ./lib/google.nix { };
bowtie = callBionix ./tools/bowtie.nix { };
bwa = callBionix ./tools/bwa.nix { };
cnvkit = callBionix ./tools/cnvkit.nix { };
compression = callBionix ./tools/compression.nix { };
crumble = callBionix ./tools/crumble.nix { };
facets = callBionix ./tools/facets.nix { };
fastqc = callBionix ./tools/fastqc.nix { };
gridss = callBionix ./tools/gridss.nix { };
infercnv = callBionix ./tools/infercnv.nix { };
kallisto = callBionix ./tools/kallisto.nix { };
mosdepth = callBionix ./tools/mosdepth.nix { };
mutect = callBionix ./tools/mutect.nix { };
minimap2 = callBionix ./tools/minimap2.nix { };
picard = callBionix ./tools/picard.nix { };
ref = callBionix ./lib/references.nix { };
samtools = callBionix ./tools/samtools.nix { };
sambamba = callBionix ./tools/sambamba.nix { };
snap = callBionix ./tools/snap.nix { };
snpeff = callBionix ./tools/snpeff.nix { };
strelka = callBionix ./tools/strelka.nix { };
ascat = callBionix ./tools/ascat.nix { };
fastp = callBionix ./tools/fastp.nix { };
octopus = callBionix ./tools/octopus.nix { };
snver = callBionix ./tools/snver.nix { };
hisat2 = callBionix ./tools/hisat2.nix { };
xenomapper = callBionix ./tools/xenomapper.nix { };
manta = callBionix ./tools/manta.nix { };
delly = callBionix ./tools/delly.nix { };
lumpy = callBionix ./tools/lumpy.nix { };
lastal = callBionix ./tools/last.nix { };
whisper = callBionix ./tools/whisper.nix { };
star = callBionix ./tools/star.nix { };
genmap = callBionix ./tools/genmap.nix { };
subread = callBionix ./tools/subread.nix { };
hatchet = callBionix ./tools/hatchet.nix { };
pizzly = callBionix ./tools/pizzly.nix { };
quip = callBionix ./tools/quip.nix { };
ampliconarchitect = callBionix ./tools/aa.nix { };
slurm-run = callPackage ./lib/slurm.nix { };
slurm-exec = f: x: y:
slurm-run x (f
(builtins.removeAttrs x [
"ppn"
"mem"
"walltime"
"partition"
"slurmFlags"
"salloc"
"srun"
])
y);
slurm = bionix.extend (self: super: { exec = super.slurm-run; });
qsub = attrs:
bionix.extend (self: super:
with self; rec {
qsubDefs = {
ppn = 1;
mem = 1;
walltime = "24:00:00";
tmpDir = "/tmp";
sleepTime = 60;
queue = null;
qsubFlags = null;
qsubPath = "/usr/bin";
} // attrs;
qsub = attrs: (callPackage ./lib/qsub.nix { }) (qsubDefs // attrs);
exec = f: x: y:
qsub (builtins.intersectAttrs qsubDefs x) (super.exec f
(builtins.removeAttrs x (builtins.attrNames qsubDefs))
y);
});
def = f: defs: attrs: f (defs // attrs);
linkOutputs = x:
let
cmds =
let
recurse = x:
if x ? type && x.type == "derivation" then
x
else if builtins.typeOf x == "set" then
linkOutputs x
else
abort "linkOutputs: unsupported type";
link = dst: src: lib.optionalString (src != null) ''
ln -s ${recurse src} $out/${lib.escapeShellArg dst}
'';
in
''
mkdir $out
${lib.concatStringsSep "\n" (lib.mapAttrsToList link x)}
'';
in
pkgs.stdenvNoCC.mkDerivation {
name = "link-outputs";
nativeBuildInputs = [ pkgs.perl ];
buildCommand = "exec sh ${pkgs.writeScript "make-links" cmds}";
passthru.linkInputs = x;
};
# Fetching files of specific type
fetchFastQ = attrs:
with types;
tagFiletype (filetype.fq { }) (fetchurl attrs);
fetchFastA = attrs:
with types;
tagFiletype (filetype.fa { }) (fetchurl attrs);
fetchFastQGZ = attrs:
with types;
tagFiletype (filetype.gz (filetype.fq { })) (fetchurl attrs);
fetchFastAGZ = attrs:
with types;
tagFiletype (filetype.gz (filetype.fa { })) (fetchurl attrs);
# Turn a multi-output derivation into a list of derivations
outputDrvs = drv: map (o: lib.getAttr o drv) drv.outputs;
# Export nixpkgs and standard library lib
pkgs = nixpkgs;
lib = nixpkgs.lib // {
inherit types;
shard = callBionix ./lib/shard.nix { };
concatMapAttrsStringsSep = s: f: a: with nixpkgs.lib; concatStringsSep s (mapAttrsToList f a);
};
stage = x@{ name, stripStorePaths ? true, multicore ? false, ... }:
(if stripStorePaths then strip else x: x)
(nixpkgs.stdenvNoCC.mkDerivation (x // {
name = "bionix-" + name;
inherit multicore;
}));
strip = drv:
let
strip-store-paths = nixpkgs.callPackage ./strip-store-paths { };
stripCommand = ''
function rewriteOutput {
find ''${!1} -type f -print0 | xargs -0 -n1 strip-store-paths
}
for o in $outputs ; do
rewriteOutput $o
done
'';
in
drv.overrideAttrs (attrs:
{ nativeBuildInputs = attrs.nativeBuildInputs or [ ] ++ [ strip-store-paths ]; } // (
if attrs ? buildCommand then {
buildCommand = attrs.buildCommand + stripCommand;
} else {
fixupPhase = (if attrs ? fixupPhase then attrs.fixupPhase else "")
+ stripCommand;
}
));
# splitting/joining
splitFile = file: drv:
stage {
name = "split-${file}";
buildCommand = "ln -s ${drv}/${file} $out";
};
split = drv: lib.mapAttrs (p: _: splitFile p drv) (builtins.readDir drv);
join = drvs:
stage {
name = "join";
buildCommand = ''
mkdir $out
${builtins.concatStringsSep "\n" (builtins.attrValues
(lib.mapAttrs (n: d: "ln -s ${d} $out/${n}") drvs))}
'';
};
each = f: drv: join (lib.mapAttrs (_: f) (split drv));
});
overlayByType = {
lambda = bionix: overlay:
bionix.extend
(self: super: nixpkgs.lib.recursiveUpdate super (overlay self super));
path = bionix: path: overlay bionix (import path);
};
overlay = bionix: overlay:
let overlayType = builtins.typeOf overlay;
in
if overlayByType ? "${overlayType}" then
overlayByType."${overlayType}" bionix overlay
else
builtins.throw ("cannot overlay type " + overlayType);
in
with nixpkgs.lib; foldl overlay bionix overlays
|
