diff --git a/docs/deepsomatic-hybrid-pacbio-illumina.md b/docs/deepsomatic-hybrid-pacbio-illumina.md index 90f717a..629917d 100644 --- a/docs/deepsomatic-hybrid-pacbio-illumina.md +++ b/docs/deepsomatic-hybrid-pacbio-illumina.md @@ -40,21 +40,21 @@ mkdir -p "${OUTPUT_DIR}" mkdir -p "${OUTPUT_DIR}/sompy_output" # Download PacBio Tumor Bam -gsutil cp gs://deepvariant/deepsomatic-case-studies/deepsomatic-chr1-case-studies/HCC1395.GRCh38.tumor.chr1.nygc.bam* ${INPUT_DIR}/ +gcloud storage cp gs://deepvariant/deepsomatic-case-studies/deepsomatic-chr1-case-studies/HCC1395.GRCh38.tumor.chr1.nygc.bam* ${INPUT_DIR}/ # Download Illumina Normal WGS -gsutil cp gs://deepvariant/deepsomatic-case-studies/deepsomatic-chr1-case-studies/HCC1395_wgs.normal.chr1.bam* ${INPUT_DIR}/ +gcloud storage cp gs://deepvariant/deepsomatic-case-studies/deepsomatic-chr1-case-studies/HCC1395_wgs.normal.chr1.bam* ${INPUT_DIR}/ # Download a reference genome -gsutil cp gs://deepvariant/deepsomatic-case-studies/deepsomatic-chr1-case-studies/GCA_000001405.15_GRCh38_no_alt_analysis_set.chr1.fna* ${INPUT_DIR}/ +gcloud storage cp gs://deepvariant/deepsomatic-case-studies/deepsomatic-chr1-case-studies/GCA_000001405.15_GRCh38_no_alt_analysis_set.chr1.fna* ${INPUT_DIR}/ # Download truth VCF -gsutil -m cp gs://deepvariant/deepsomatic-case-studies/SEQC2-S1395-truth/High-Confidence_Regions_v1.2.bed \ +gcloud storage cp gs://deepvariant/deepsomatic-case-studies/SEQC2-S1395-truth/High-Confidence_Regions_v1.2.bed \ gs://deepvariant/deepsomatic-case-studies/SEQC2-S1395-truth/high-confidence_sINDEL_sSNV_in_HC_regions_v1.2.1.merged.vcf.gz* \ gs://deepvariant/deepsomatic-case-studies/SEQC2-S1395-truth/seqc2_hg38.exome_regions.bed ${INPUT_DIR} # Download the model -gsutil -m cp gs://deepvariant/models/experimental/deepsomatic_hybrid/exp_157994267/* ${INPUT_DIR} +gcloud storage cp gs://deepvariant/models/experimental/deepsomatic_hybrid/exp_157994267/* ${INPUT_DIR} ``` ## Running DeepSomatic with one command