prepare_cancer_giab

prepare.sh

#!/bin/bash
export OUT=/var/www/html/jbrowse2
sudo apt-get update
sudo apt-get install nodejs wget apache2 tabix samtools minimap2
sudo service apache2 start
## confirm node.js greater than or equal to v18 is installed
node --version
sudo npm install -g @jbrowse/cli
## confirm that the jbrowse CLI is installed
jbrowse --version
## "jbrowse create" downloads and unzips the latest version of JBrowse 2, and then we move it to a web directory
jbrowse create tmpdir
sudo mv tmpdir $OUT

## add the human genome
jbrowse add-assembly https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit --out $OUT

## add the cancer genome in a bottle
jbrowse add-track --out $OUT --category "Cancer GIAB" https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIH_HiFi-HiC_Wakhan-CNA_20240424/bed_output/HG008_HiFi_HiC_copynumbers_segments.bed
jbrowse add-track --out $OUT --category "Cancer GIAB" https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIH_HiFi-HiC_Wakhan-CNA_20240424/bed_output/HG008_HiFi_HiC_loh_segments.bed
jbrowse add-track --out $OUT --category "Cancer GIAB" https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIST_HG008-T_somatic-stvar-CNV_DraftBenchmark_V0.4-20250714/GRCh38_HG008-T-V0.4_somatic-CNV_PASS.draftbenchmark.calls.bed 
jbrowse add-track --out $OUT --category "Cancer GIAB" https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIST_HG008-T_somatic-stvar-CNV_DraftBenchmark_V0.4-20250714/GRCh38_HG008-T-V0.4_somatic-stvar_PASS.draftbenchmark.vcf.gz
jbrowse add-track --out $OUT --category "Cancer GIAB" https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIH_HiFi_mm2_mapping/HG008-T_PacBio-HiFi-Revio_20240125_116x_GRCh38-GIABv3_mm2.bam
jbrowse add-track --out $OUT --category "Cancer GIAB" https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIH_HiFi_mm2_mapping/HG008-N-P_PacBio-HiFi-Revio_20240125_35x_GRCh38-GIABv3_mm2.bam