From 2d7a2b001936a8a047118af0f99a9cbfd38d258a Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Sun, 19 Jun 2022 08:27:00 +1000
Subject: hatchet: include gurobi dependency if needed
---
tools/hatchet-call.nix | 257 +++++++++++++++++++++++++------------------------
1 file changed, 132 insertions(+), 125 deletions(-)
(limited to 'tools')
diff --git a/tools/hatchet-call.nix b/tools/hatchet-call.nix
index c99e664..55414fe 100644
--- a/tools/hatchet-call.nix
+++ b/tools/hatchet-call.nix
@@ -1,131 +1,138 @@
-{ bionix
-, gurobiLicense ? null
-, count_reads ? true
-, genotype_snps ? true
-, count_alleles ? true
-, combine_counts ? true
-, cluster_bins ? true
-, plot_bins ? true
-, compute_cn ? true
-, plot_cn ? true
-, size ? "50kb"
-, mincov ? 8
-, maxcov ? 300
-, snps
-, phase ? "None"
-, diploidbaf ? 0.08
-, tolerancerdr ? 0.15
-, tolerancebaf ? 0.04
-, sizethreshold ? 0.01
-, figsize ? "6,3"
-, clones ? [ 2 6 ]
-, seeds ? 400
-, minprop ? 0.03
-, diploidcmax ? 6
-, tetraploidcmax ? 12
-, ghostprop ? 0.35
-, limitinc ? 0.6
-, blocklength ? "50kb"
+{
+ bionix,
+ gurobiLicense ? null,
+ count_reads ? true,
+ genotype_snps ? true,
+ count_alleles ? true,
+ combine_counts ? true,
+ cluster_bins ? true,
+ plot_bins ? true,
+ compute_cn ? true,
+ plot_cn ? true,
+ size ? "50kb",
+ mincov ? 8,
+ maxcov ? 300,
+ snps,
+ phase ? "None",
+ diploidbaf ? 0.08,
+ tolerancerdr ? 0.15,
+ tolerancebaf ? 0.04,
+ sizethreshold ? 0.01,
+ figsize ? "6,3",
+ clones ? [2 6],
+ seeds ? 400,
+ minprop ? 0.03,
+ diploidcmax ? 6,
+ tetraploidcmax ? 12,
+ ghostprop ? 0.35,
+ limitinc ? 0.6,
+ blocklength ? "50kb",
}:
-
with bionix;
with lib;
with types;
-
-{ normal, tumours }:
-
-let getRef = matchFiletype "hatchet" { bam = { ref, ... }: ref; };
-in
-
-assert all (x: getRef normal == getRef x) tumours;
-
-let
- ref = getRef normal;
-
- ini = pkgs.writeText "hatchet.ini" (generators.toINI { } {
- run = {
- inherit count_reads genotype_snps count_alleles combine_counts cluster_bins plot_bins compute_cn plot_cn;
- reference = "${lnRef ref}/ref.fa";
- normal = "${lnBam normal}/input.bam";
- bams = concatMapStringsSep " " (x: "${lnBam x}/input.bam") tumours;
- samples = "@SAMPLES@";
- output = "./out";
- processes = "@PROCESSES@";
- };
-
- count_reads = { inherit size; };
- genotype_snps = {
- inherit mincov maxcov;
- snps = "${lnVcfBz snps}/vcf.bgz";
- };
-
- count_alleles = { inherit mincov maxcov; };
- combine_counts = { inherit blocklength phase; };
- cluster_bins = { inherit diploidbaf tolerancerdr tolerancebaf; };
- plot_bins = { inherit sizethreshold figsize; };
- compute_cn = {
- inherit seeds minprop diploidcmax tetraploidcmax ghostprop limitinc;
- clones = concatMapStringsSep "," builtins.toString clones;
- };
-
- });
-
- lnRef = ref: linkOutputs {
- "ref.fa" = ref;
- "ref.fa.fai" = samtools.faidx { } ref;
- "ref.dict" = samtools.dict { } ref;
- };
-
- lnBam = bam:
- linkOutputs {
- "input.bam" = bam;
- "input.bam.bai" = samtools.index { } bam;
- };
-
- lnVcfBz = vcf:
- let bz = compression.bgzip { } vcf;
+ {
+ normal,
+ tumours,
+ }: let
+ getRef = matchFiletype "hatchet" {bam = {ref, ...}: ref;};
+ in
+ assert all (x: getRef normal == getRef x) tumours; let
+ ref = getRef normal;
+
+ ini = pkgs.writeText "hatchet.ini" (generators.toINI {} {
+ run = {
+ inherit count_reads genotype_snps count_alleles combine_counts cluster_bins plot_bins compute_cn plot_cn;
+ reference = "${lnRef ref}/ref.fa";
+ normal = "${lnBam normal}/input.bam";
+ bams = concatMapStringsSep " " (x: "${lnBam x}/input.bam") tumours;
+ samples = "@SAMPLES@";
+ output = "./out";
+ processes = "@PROCESSES@";
+ };
+
+ count_reads = {inherit size;};
+ genotype_snps = {
+ inherit mincov maxcov;
+ snps = "${lnVcfBz snps}/vcf.bgz";
+ };
+
+ count_alleles = {inherit mincov maxcov;};
+ combine_counts = {inherit blocklength phase;};
+ cluster_bins = {inherit diploidbaf tolerancerdr tolerancebaf;};
+ plot_bins = {inherit sizethreshold figsize;};
+ compute_cn = {
+ inherit seeds minprop diploidcmax tetraploidcmax ghostprop limitinc;
+ clones = concatMapStringsSep "," builtins.toString clones;
+ };
+ });
+
+ lnRef = ref:
+ linkOutputs {
+ "ref.fa" = ref;
+ "ref.fa.fai" = samtools.faidx {} ref;
+ "ref.dict" = samtools.dict {} ref;
+ };
+
+ lnBam = bam:
+ linkOutputs {
+ "input.bam" = bam;
+ "input.bam.bai" = samtools.index {} bam;
+ };
+
+ lnVcfBz = vcf: let
+ bz = compression.bgzip {} vcf;
+ in
+ linkOutputs {
+ "vcf.bgz" = bz;
+ "vcf.bgz.tbi" = samtools.tabix {} bz;
+ };
+
+ getSN = let
+ script = pkgs.writeText "getSN.awk" ''
+ BEGIN{
+ FS=":"
+ RS="[ \t\n]"
+ }
+ $1=="SM"{print $2; exit}
+ '';
+ in
+ pkgs.writeShellScriptBin "getSN" ''
+ exec samtools view -H "$1" | awk -f ${script}
+ '';
in
- linkOutputs {
- "vcf.bgz" = bz;
- "vcf.bgz.tbi" = samtools.tabix { } bz;
- };
-
- getSN =
- let
- script = pkgs.writeText "getSN.awk" ''
- BEGIN{
- FS=":"
- RS="[ \t\n]"
+ stage
+ ({
+ name = "HATCHet";
+ buildInputs =
+ [hatchet.app getSN pkgs.samtools pkgs.bcftools]
+ ++ (
+ if gurobiLicense == null
+ then [pkgs.cbc]
+ else [pkgs.gurobi]
+ );
+ buildCommand = ''
+ # Get tumour names
+ names="${concatMapStringsSep " " (x: "$(getSN ${x})") tumours}"
+
+ # macro substitute ini file
+ substitute ${ini} hatchet.ini \
+ --replace "@PROCESSES@" "$NIX_BUILD_CORES" \
+ --replace "@SAMPLES@" "$names"
+
+ hatchet run hatchet.ini
+
+ cp -r out $out
+ '';
+ passthru.multicore = true;
}
- $1=="SM"{print $2; exit}
- '';
- in
- pkgs.writeShellScriptBin "getSN" ''
- exec samtools view -H "$1" | awk -f ${script}
- '';
-
-in
-stage
- ({
- name = "HATCHet";
- buildInputs = [ hatchet.app getSN pkgs.samtools pkgs.bcftools ] ++ optional (gurobiLicense == null) pkgs.cbc;
- buildCommand = ''
- # Get tumour names
- names="${concatMapStringsSep " " (x: "$(getSN ${x})") tumours}"
-
- # macro substitute ini file
- substitute ${ini} hatchet.ini \
- --replace "@PROCESSES@" "$NIX_BUILD_CORES" \
- --replace "@SAMPLES@" "$names"
-
- hatchet run hatchet.ini
-
- cp -r out $out
- '';
- passthru.multicore = true;
- } // (if gurobiLicense != null then {
- GRB_LICENSE_FILE = gurobiLicense;
- HATCHET_COMPUTE_CN_SOLVER = "gurobi";
- } else {
- HATCHET_COMPUTE_CN_SOLVER = "cbc";
- }))
+ // (
+ if gurobiLicense != null
+ then {
+ GRB_LICENSE_FILE = gurobiLicense;
+ HATCHET_COMPUTE_CN_SOLVER = "gurobi";
+ }
+ else {
+ HATCHET_COMPUTE_CN_SOLVER = "cbc";
+ }
+ ))
--
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