PhyloWGS containerization

.gitignore

@@ -1,4 +1,9 @@
 *.o
 *.pyc
 venv
-env
+*out
+*json
+*txt
+*noXY*
+input_list*
+run*sh

Dockerfile

@@ -0,0 +1,17 @@
+FROM ubuntu 
+
+RUN apt-get update && apt-get install -y gfortran build-essential \
+make gcc build-essential python python-dev wget libgsl23 \
+gsl-bin libgsl-dev python-pip git \
+libblas-dev liblapack-dev
+
+RUN pip install PyVCF 
+
+RUN pip install numpy scipy 
+
+WORKDIR /opt 
+
+RUN git clone https://github.com/morrislab/smchet-challenge.git && cd smchet-challenge && git checkout master
+RUN git clone https://github.com/morrislab/phylowgs.git && cd phylowgs && git checkout master
+
+RUN cd phylowgs && g++ -o mh.o -O3 mh.cpp util.cpp `gsl-config --cflags --libs`

multievolve.cwl

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+cwlVersion: v1.0
+class: CommandLineTool
+label: Multievolve
+baseCommand: ["python", "/opt/phylowgs/multievolve.py"]
+requirements:
+  - class: DockerRequirement
+    dockerPull: smcheteval/phylowgs:0.1
+
+inputs:
+  num_chains:
+    type: int
+    default: 16
+    inputBinding:
+      prefix: --num-chains
+
+  random_seeds:
+    type: int[]
+    default: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16]
+    inputBinding:
+      prefix: --random-seeds
+
+  chain_inclusion_factor:
+    type: float
+    default: 1.1
+    inputBinding:
+      prefix: --chain-inclusion-factor
+
+  mcmc:
+    type: int
+    default: 5000
+    inputBinding:
+      prefix: --mcmc-samples
+
+  burnin:
+    type: int
+    default: 2000
+    inputBinding:
+      prefix: --burnin-samples
+
+  ssms:
+    type: File
+    inputBinding:
+      prefix: --ssms
+
+  cnvs:
+    type: File
+    inputBinding:
+      prefix: --cnvs
+
+  output_dir:
+    type: string
+    default: ./
+    inputBinding:
+      prefix: --output-dir
+
+outputs:
+  tree_file:
+    type: File
+    outputBinding:
+      glob: trees.zip
+

parser/create_phylowgs_inputs.cwl

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+cwlVersion: v1.0
+class: CommandLineTool
+label: PhyloWGS Input Prep
+baseCommand: ["python","/opt/phylowgs/parser/create_phylowgs_inputs.py"]
+requirements:
+  - class: DockerRequirement
+    dockerPull: smcheteval/phylowgs:0.1
+
+inputs:
+  cnvs:
+    type: File
+    inputBinding:
+      prefix: "--cnvs s1="
+      separate: false
+
+  output_cnvs:
+    type: string
+    default: cnv_data.txt
+    inputBinding:
+      prefix: --output-cnvs
+
+  output_variants:
+    type: string
+    default: ssm_data.txt
+    inputBinding:
+      prefix: --output-variants
+
+  vcf_type:
+    type: string
+    default: "s1=mutect_smchet"
+    inputBinding:
+      prefix: --vcf-type
+
+  vcf_files:
+    type: File
+    inputBinding:
+      prefix: "s1="
+      separate: false
+      position: 5
+
+outputs:
+  multievolve_cnvs:
+    type: File
+    outputBinding:
+      glob: $(inputs.output_cnvs)
+
+  multievolve_snvs:
+    type: File
+    outputBinding:
+      glob: $(inputs.output_variants)

parser/parse_cnvs.cwl

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+cwlVersion: v1.0
+class: CommandLineTool
+baseCommand: ["python","/opt/phylowgs/parser/parse_cnvs.py"]
+requirements:
+  - class: DockerRequirement
+    dockerPull: smcheteval/phylowgs:0.1
+
+inputs:
+  cnv_format:
+    type: string
+    default: battenberg-smchet
+    inputBinding:
+      prefix: --cnv-format
+
+  cellularity:
+    type: float
+    default: None
+    inputBinding:
+      prefix: --cellularity
+
+  cnv_output:
+    type: string
+    default: cnvs.txt
+    inputBinding:
+      prefix: --cnv-output
+
+  cnv_file:
+    type: File
+    inputBinding:
+      position: 4
+
+outputs:
+  parser_output:
+    type: File
+    outputBinding:
+      glob: $(inputs.cnv_output)

parser/run_create_inputs.sh

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+#!/bin/bash
+# run_create_inputs.sh
+#SBATCH --partition=exacloud
+#SBATCH --output=parser-%j.out
+#SBATCH --error=parser-%j.err
+#SBATCH --job-name=run_smchet_create_inputs
+#SBATCH --gres disk:1024
+#SBATCH --mincpus=1
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=1G
+#SBATCH --time=00:45:00
+
+source /home/groups/EllrottLab/activate_conda
+ABS_PATH="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+sbatch cwltool $ABS_PATH/create_phylowgs_inputs.cwl $ABS_PATH/run_create_inputs.json

parser/run_parser.sh

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+#!/bin/bash
+# run_parser.sh
+#SBATCH --partition=exacloud
+#SBATCH --output=parser-%j.out
+#SBATCH --error=parser-%j.err
+#SBATCH --job-name=run_smchet_parser
+#SBATCH --gres disk:1024
+#SBATCH --mincpus=1
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=1G
+#SBATCH --time=00:45:00
+
+source /home/groups/EllrottLab/activate_conda
+ABS_PATH="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+sbatch cwltool --debug $ABS_PATH/parse_cnvs.cwl $ABS_PATH/parse_cnvs.json

phylowgs.cwl

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+cwlVersion: v1.0
+class: Workflow
+
+requirements:
+  - class: SubworkflowFeatureRequirement
+  - class: StepInputExpressionRequirement
+
+inputs:
+  ssmFile:
+    type: File
+  cnvFile:
+    type: File
+  cellFxn:
+    type: float
+
+steps:
+  parse:
+    run: ./parser/parse_cnvs.cwl
+    in:
+      cellularity: cellFxn
+      cnv_file: cnvFile
+    out:
+      - parser_output
+
+  prep_inputs:
+    run: ./parser/create_phylowgs_inputs.cwl
+    in:
+      cnvs: parse/parser_output
+      vcf_files: ssmFile
+    out:
+      - multievolve_snvs
+      - multievolve_cnvs
+
+  multievolve:
+    run: ./multievolve.cwl
+    in:
+      ssms: prep_inputs/multievolve_snvs
+      cnvs: prep_inputs/multievolve_cnvs
+    out:
+      - tree_file
+
+  write_results:
+    run: ./write_results.cwl
+    in: 
+      tree_file: multievolve/tree_file
+    out:
+      - summary_results
+      - mutlist_results
+      - mutass_results
+
+  write_report:
+    run: ../smchet-challenge/create-smchet-report/write_report.cwl
+    in:
+      tree_summary: write_results/summary_results
+      mutation_list: write_results/mutlist_results
+      mutation_assignment: write_results/mutass_results
+    out:
+      - cellularity
+      - population
+      - proportion
+      - cluster_assignment
+      - cocluster_assignment
+
+outputs:
+  cellularity_predfile:
+    type: File
+    outputSource: write_report/cellularity
+  population_predfile:
+    type: File
+    outputSource: write_report/population
+  proportion_predfile:
+    type: File
+    outputSource: write_report/proportion
+  cluster_assignment_predfile:
+    type: File
+    outputSource: write_report/cluster_assignment
+  cocluster_assignment_predfile:
+    type: File
+    outputSource: write_report/cocluster_assignment

run_multi.sh

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+#!/bin/bash
+# run_multi.sh
+#SBATCH --partition=exacloud
+#SBATCH --output=multievolve-%j.out
+#SBATCH --error=multievolve-%j.err
+#SBATCH --job-name=run_smchet_multievolve
+#SBATCH --gres disk:1024
+#SBATCH --mincpus=1
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=1G
+#SBATCH --time=06:00:00
+
+source /home/groups/EllrottLab/activate_conda
+ABS_PATH="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+sbatch cwltool $ABS_PATH/multievolve.cwl $ABS_PATH/run_multi.json

run_phylowgs.sh

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+#!/bin/bash
+
+###https://github.com/Sage-Bionetworks/SMC-Het-Challenge-Examples/blob/master/PhyloWGS/command/run_phylowgs.sh
+
+BATTEN=$1
+VCF=$2
+CELL=$3
+PUR=(`sed "2q;d" ${CELL}`)
+SNV_CALLER="mutect_smchet"
+CNV_CALLER="battenberg-smchet"
+MCMC=5000
+BURNIN=2000
+NCHAINS=16
+RANDOM_SEED="`seq 1 ${NCHAINS}`"
+#TODO: Fix cellularity
+#TODO: subsampling
+#if $subsample.run == "yes":
+#--sample-size ${subsample.count}
+#end if
+#TODO: normal-cn
+#if $only_normal_cn
+#--only-normal-cn 
+#end if
+
+python /opt/phylowgs/parser/parse_cnvs.py --cnv-format $CNV_CALLER --cellularity $PUR --cnv-output cnvs.txt $BATTEN
+
+python /opt/phylowgs/parser/create_phylowgs_inputs.py --cnvs s1=cnvs.txt --output-cnvs cnv_data.txt --output-variants ssm_data.txt --vcf-type s1=$SNV_CALLER s1=$VCF
+python /opt/phylowgs/multievolve.py --num-chains $NCHAINS --ssms ssm_data.txt --cnvs cnv_data.txt --burnin-samples $BURNIN --mcmc-samples $MCMC -r $RANDOM_SEED
+
+python /opt/phylowgs/write_results.py tumour /opt/chains/trees.zip trees.json.gz mutations.json.gz mutation_assignments.json.gz
+
+PYTHONPATH='/opt/phylowgs/' python /opt/smchet-challenge/create-smchet-report/write_report.py trees.json.gz mutations.json.gz mutation_assignments.json.gz /opt/outputs

run_results.sh

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+#!/bin/bash
+# run_results.sh
+#SBATCH --partition=exacloud
+#SBATCH --output=results-%j.out
+#SBATCH --error=results-%j.err
+#SBATCH --job-name=run_smchet_results
+#SBATCH --gres disk:1024
+#SBATCH --mincpus=1
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=1G
+#SBATCH --time=00:45:00
+
+source /home/groups/EllrottLab/activate_conda
+ABS_PATH="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+sbatch cwltool --debug $ABS_PATH/write_results.cwl $ABS_PATH/write_results.json