#!/usr/bin/env bash # Bulk download script for GSE255844 # Generated from Yeo Lab Publications Database # Total files: 23 OUTDIR="GSE255844" mkdir -p "$OUTDIR" cd "$OUTDIR" # --- GEO supplementary files --- wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE255nnn/GSE255844/suppl/GSE255844_RAW.tar" -O "GSE255844_RAW.tar" # --- SRA run files --- # Tip: use 'fasterq-dump' from SRA Toolkit for FASTQ conversion # with optional renaming to original submitted FASTQ names. # Set to 1 to rename SRR outputs (e.g. SRR_1.fastq.gz -> sample_R1.fastq.gz) RENAME_SRA_TO_ORIGINAL=1 _compress_if_exists() { local stem="$1" if [ -f "${stem}.fastq" ]; then gzip -f "${stem}.fastq" echo "${stem}.fastq.gz" return 0 fi if [ -f "${stem}.fq" ]; then gzip -f "${stem}.fq" echo "${stem}.fq.gz" return 0 fi return 1 } # Option A: Download via SRA Toolkit (recommended) fasterq-dump --split-files "SRR27982876" gz1="$(_compress_if_exists 'SRR27982876_1' || true)" gz2="$(_compress_if_exists 'SRR27982876_2' || true)" gzs="$(_compress_if_exists 'SRR27982876' || true)" fasterq-dump --split-files "SRR27982877" gz1="$(_compress_if_exists 'SRR27982877_1' || true)" gz2="$(_compress_if_exists 'SRR27982877_2' || true)" gzs="$(_compress_if_exists 'SRR27982877' || true)" fasterq-dump --split-files "SRR27982878" gz1="$(_compress_if_exists 'SRR27982878_1' || true)" gz2="$(_compress_if_exists 'SRR27982878_2' || true)" gzs="$(_compress_if_exists 'SRR27982878' || true)" fasterq-dump --split-files "SRR27982879" gz1="$(_compress_if_exists 'SRR27982879_1' || true)" gz2="$(_compress_if_exists 'SRR27982879_2' || true)" gzs="$(_compress_if_exists 'SRR27982879' || true)" fasterq-dump --split-files "SRR27982880" gz1="$(_compress_if_exists 'SRR27982880_1' || true)" gz2="$(_compress_if_exists 'SRR27982880_2' || true)" gzs="$(_compress_if_exists 'SRR27982880' || true)" fasterq-dump --split-files "SRR27982881" gz1="$(_compress_if_exists 'SRR27982881_1' || true)" gz2="$(_compress_if_exists 'SRR27982881_2' || true)" gzs="$(_compress_if_exists 'SRR27982881' || true)" fasterq-dump --split-files "SRR27982882" gz1="$(_compress_if_exists 'SRR27982882_1' || true)" gz2="$(_compress_if_exists 'SRR27982882_2' || true)" gzs="$(_compress_if_exists 'SRR27982882' || true)" fasterq-dump --split-files "SRR27982883" gz1="$(_compress_if_exists 'SRR27982883_1' || true)" gz2="$(_compress_if_exists 'SRR27982883_2' || true)" gzs="$(_compress_if_exists 'SRR27982883' || true)" fasterq-dump --split-files "SRR27982884" gz1="$(_compress_if_exists 'SRR27982884_1' || true)" gz2="$(_compress_if_exists 'SRR27982884_2' || true)" gzs="$(_compress_if_exists 'SRR27982884' || true)" fasterq-dump --split-files "SRR27982885" gz1="$(_compress_if_exists 'SRR27982885_1' || true)" gz2="$(_compress_if_exists 'SRR27982885_2' || true)" gzs="$(_compress_if_exists 'SRR27982885' || true)" # Option B: Direct download (larger .sra files) curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-run-30/SRR027/27982/SRR27982876/SRR27982876.1" curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-run-30/SRR027/27982/SRR27982877/SRR27982877.1" curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-run-30/SRR027/27982/SRR27982878/SRR27982878.1" curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-run-30/SRR027/27982/SRR27982879/SRR27982879.1" curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-run-30/SRR027/27982/SRR27982880/SRR27982880.1" curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-run-30/SRR027/27982/SRR27982881/SRR27982881.1" curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-run-30/SRR027/27982/SRR27982882/SRR27982882.1" curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-run-30/SRR027/27982/SRR27982883/SRR27982883.1" curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-run-30/SRR027/27982/SRR27982884/SRR27982884.1" curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-run-30/SRR027/27982/SRR27982885/SRR27982885.1" # --- Additional data files --- curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-run-30/SRR027/27982/SRR27982885/SRR27982885.1" curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-run-30/SRR027/27982/SRR27982884/SRR27982884.1" curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-run-30/SRR027/27982/SRR27982883/SRR27982883.1" curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-run-30/SRR027/27982/SRR27982882/SRR27982882.1" curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-run-30/SRR027/27982/SRR27982881/SRR27982881.1" curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-run-30/SRR027/27982/SRR27982880/SRR27982880.1" curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-run-30/SRR027/27982/SRR27982877/SRR27982877.1" curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-run-30/SRR027/27982/SRR27982876/SRR27982876.1" curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-run-30/SRR027/27982/SRR27982879/SRR27982879.1" curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-run-30/SRR027/27982/SRR27982878/SRR27982878.1" curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-run-30/SRR027/27982/SRR27982883/SRR27982883.1" curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-run-30/SRR027/27982/SRR27982884/SRR27982884.1" echo "Download complete. Files saved to $OUTDIR"