QuickStarts from the terminal¶

Use these commands when you want a scripted run without browser setup. First install a backend and download and verify the reads in QuickStart 1 or QuickStart 2. Use a new project folder; these commands replace the browser steps in those guides.

QuickStart 1¶

After downloading, these replace browser setup. For Docker, use --backend docker in setup/run plus your installed --image. To match browser preservation metadata, append --variant-specimen-type fresh or --variant-specimen-type ffpe to setup, according to specimen records.

Illumina — terminal only¶

cd /path/to/my/analyses_dir/
oncotracer setup --non-interactive \
  --project "$PWD/oncotracer-quickstart1/illumina" --mode illumina --analysis cna \
  --sample-name ERR12341627 --status tumor \
  --fastq-1 "$PWD/oncotracer-quickstart1/input/illumina/ERR12341627_1.fastq.gz" \
  --fastq-2 "$PWD/oncotracer-quickstart1/input/illumina/ERR12341627_2.fastq.gz" \
  --backend conda --threads 4
oncotracer check --config "$PWD/oncotracer-quickstart1/illumina/config/run.yml"
oncotracer run --backend conda \
  --config "$PWD/oncotracer-quickstart1/illumina/config/run.yml"

ONT — terminal only¶

cd /path/to/my/analyses_dir/
oncotracer setup --non-interactive \
  --project "$PWD/oncotracer-quickstart1/ont" --mode ont --analysis cna \
  --reads-folder "$PWD/oncotracer-quickstart1/input/fastq_pass" \
  --barcodes barcode01 --sample-names DRR165691 --backend conda --threads 4
oncotracer check --config "$PWD/oncotracer-quickstart1/ont/config/run.yml"
oncotracer run --backend conda \
  --config "$PWD/oncotracer-quickstart1/ont/config/run.yml"

QuickStart 2¶

Terminal / headless version: after the downloads above, run these blocks instead of browser setup. They create the same three-library project without questions. Use only one setup method per project. Append --variant-specimen-type fresh or --variant-specimen-type ffpe to setup to record the same preservation selected in the browser, using specimen records.

Create the samplesheet with absolute paths. Paste the final CSV line too. cat > replaces the CSV if it already exists.

cd /path/to/my/analyses_dir/
cat > "$PWD/oncotracer-quickstart2/input/samplesheet.csv" <<CSV
sample,fastq_1,fastq_2,status
HCC1143_DMSO,"$PWD/oncotracer-quickstart2/input/HCC1143_DMSO_R1.fastq.gz","$PWD/oncotracer-quickstart2/input/HCC1143_DMSO_R2.fastq.gz",tumor
HCC1143_BEZ235,"$PWD/oncotracer-quickstart2/input/HCC1143_BEZ235_R1.fastq.gz","$PWD/oncotracer-quickstart2/input/HCC1143_BEZ235_R2.fastq.gz",tumor
HCC1143_TRAMETINIB,"$PWD/oncotracer-quickstart2/input/HCC1143_TRAMETINIB_R1.fastq.gz","$PWD/oncotracer-quickstart2/input/HCC1143_TRAMETINIB_R2.fastq.gz",tumor
CSV

Create settings without starting analysis:

cd /path/to/my/analyses_dir/
oncotracer setup --non-interactive \
  --project "$PWD/oncotracer-quickstart2/analysis" \
  --hg38_build \
  --mode illumina --analysis cna --backend conda \
  --samplesheet "$PWD/oncotracer-quickstart2/input/samplesheet.csv" \
  --threads 4

Check should list all three names. Resolve errors before running:

cd /path/to/my/analyses_dir/
oncotracer check --config "$PWD/oncotracer-quickstart2/analysis/config/run.yml"
oncotracer run --backend conda \
  --config "$PWD/oncotracer-quickstart2/analysis/config/run.yml"

Use the corresponding backend for Docker or Apptainer.

References and resuming¶

The examples prepare the required hg38 indexes when the analysis starts. To reuse a prepared reference, add --hg38_build /data/shared-reference to setup; for QuickStart 2, replace its bare --hg38_build flag. Illumina needs BWA indexes and ONT needs minimap2 indexes. Use --build_reference instead to build indexes locally. See genome indexes.

After interruption, repeat only the saved project's oncotracer check and oncotracer run commands. Valid completed work is reused; omit --force. See run, stop and resume for progress and stop controls, or headless servers for SSH and persistent terminal sessions.