#!/usr/bin/env bash # Bulk download script for GSE166404 # Generated from Yeo Lab Publications Database # Total files: 61 OUTDIR="GSE166404" mkdir -p "$OUTDIR" cd "$OUTDIR" # --- GEO supplementary files --- wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE166nnn/GSE166404/suppl/GSE166404_RAW.tar" -O "GSE166404_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 "${stem}.fq.gz" return 0 fi return 1 } # Option A: Download via SRA Toolkit (recommended) fasterq-dump --split-files "SRR13663731" gz1="$(_compress_if_exists 'SRR13663731_1' || true)" gz2="$(_compress_if_exists 'SRR13663731_2' || true)" gzs="$(_compress_if_exists 'SRR13663731' || true)" fasterq-dump --split-files "SRR13663732" gz1="$(_compress_if_exists 'SRR13663732_1' || true)" gz2="$(_compress_if_exists 'SRR13663732_2' || true)" gzs="$(_compress_if_exists 'SRR13663732' || true)" fasterq-dump --split-files "SRR13663733" gz1="$(_compress_if_exists 'SRR13663733_1' || true)" gz2="$(_compress_if_exists 'SRR13663733_2' || true)" gzs="$(_compress_if_exists 'SRR13663733' || true)" fasterq-dump --split-files "SRR13663734" gz1="$(_compress_if_exists 'SRR13663734_1' || true)" gz2="$(_compress_if_exists 'SRR13663734_2' || true)" gzs="$(_compress_if_exists 'SRR13663734' || true)" fasterq-dump --split-files "SRR13663735" gz1="$(_compress_if_exists 'SRR13663735_1' || true)" gz2="$(_compress_if_exists 'SRR13663735_2' || true)" gzs="$(_compress_if_exists 'SRR13663735' || true)" fasterq-dump --split-files "SRR13663736" gz1="$(_compress_if_exists 'SRR13663736_1' || true)" gz2="$(_compress_if_exists 'SRR13663736_2' || true)" gzs="$(_compress_if_exists 'SRR13663736' || true)" fasterq-dump --split-files "SRR13663737" gz1="$(_compress_if_exists 'SRR13663737_1' || true)" gz2="$(_compress_if_exists 'SRR13663737_2' || true)" gzs="$(_compress_if_exists 'SRR13663737' || true)" fasterq-dump --split-files "SRR13663738" gz1="$(_compress_if_exists 'SRR13663738_1' || true)" gz2="$(_compress_if_exists 'SRR13663738_2' || true)" gzs="$(_compress_if_exists 'SRR13663738' || true)" fasterq-dump --split-files "SRR13663739" gz1="$(_compress_if_exists 'SRR13663739_1' || true)" gz2="$(_compress_if_exists 'SRR13663739_2' || true)" gzs="$(_compress_if_exists 'SRR13663739' || true)" fasterq-dump --split-files "SRR13663740" gz1="$(_compress_if_exists 'SRR13663740_1' || true)" gz2="$(_compress_if_exists 'SRR13663740_2' || true)" gzs="$(_compress_if_exists 'SRR13663740' || true)" fasterq-dump --split-files "SRR13663741" gz1="$(_compress_if_exists 'SRR13663741_1' || true)" gz2="$(_compress_if_exists 'SRR13663741_2' || true)" gzs="$(_compress_if_exists 'SRR13663741' || true)" fasterq-dump --split-files "SRR13663742" gz1="$(_compress_if_exists 'SRR13663742_1' || true)" gz2="$(_compress_if_exists 'SRR13663742_2' || true)" gzs="$(_compress_if_exists 'SRR13663742' || true)" fasterq-dump --split-files "SRR13663743" gz1="$(_compress_if_exists 'SRR13663743_1' || true)" gz2="$(_compress_if_exists 'SRR13663743_2' || true)" gzs="$(_compress_if_exists 'SRR13663743' || true)" fasterq-dump --split-files "SRR13663744" gz1="$(_compress_if_exists 'SRR13663744_1' || true)" gz2="$(_compress_if_exists 'SRR13663744_2' || true)" gzs="$(_compress_if_exists 'SRR13663744' || true)" fasterq-dump --split-files "SRR13663745" gz1="$(_compress_if_exists 'SRR13663745_1' || true)" gz2="$(_compress_if_exists 'SRR13663745_2' || true)" gzs="$(_compress_if_exists 'SRR13663745' || true)" fasterq-dump --split-files "SRR13663746" gz1="$(_compress_if_exists 'SRR13663746_1' || true)" gz2="$(_compress_if_exists 'SRR13663746_2' || true)" gzs="$(_compress_if_exists 'SRR13663746' || true)" fasterq-dump --split-files "SRR13663747" gz1="$(_compress_if_exists 'SRR13663747_1' || true)" gz2="$(_compress_if_exists 'SRR13663747_2' || true)" gzs="$(_compress_if_exists 'SRR13663747' || true)" fasterq-dump --split-files "SRR13663748" gz1="$(_compress_if_exists 'SRR13663748_1' || true)" gz2="$(_compress_if_exists 'SRR13663748_2' || true)" gzs="$(_compress_if_exists 'SRR13663748' || true)" fasterq-dump --split-files "SRR13663749" gz1="$(_compress_if_exists 'SRR13663749_1' || true)" gz2="$(_compress_if_exists 'SRR13663749_2' || true)" gzs="$(_compress_if_exists 'SRR13663749' || true)" fasterq-dump --split-files "SRR13663750" gz1="$(_compress_if_exists 'SRR13663750_1' || true)" gz2="$(_compress_if_exists 'SRR13663750_2' || true)" gzs="$(_compress_if_exists 'SRR13663750' || true)" fasterq-dump --split-files "SRR13663751" gz1="$(_compress_if_exists 'SRR13663751_1' || true)" gz2="$(_compress_if_exists 'SRR13663751_2' || true)" gzs="$(_compress_if_exists 'SRR13663751' || true)" fasterq-dump --split-files "SRR13663752" gz1="$(_compress_if_exists 'SRR13663752_1' || true)" gz2="$(_compress_if_exists 'SRR13663752_2' || true)" gzs="$(_compress_if_exists 'SRR13663752' || true)" fasterq-dump --split-files "SRR13663753" gz1="$(_compress_if_exists 'SRR13663753_1' || true)" gz2="$(_compress_if_exists 'SRR13663753_2' || true)" gzs="$(_compress_if_exists 'SRR13663753' || true)" fasterq-dump --split-files "SRR13663754" gz1="$(_compress_if_exists 'SRR13663754_1' || true)" gz2="$(_compress_if_exists 'SRR13663754_2' || true)" gzs="$(_compress_if_exists 'SRR13663754' || true)" fasterq-dump --split-files "SRR13663755" gz1="$(_compress_if_exists 'SRR13663755_1' || true)" gz2="$(_compress_if_exists 'SRR13663755_2' || true)" gzs="$(_compress_if_exists 'SRR13663755' || true)" fasterq-dump --split-files "SRR13663756" gz1="$(_compress_if_exists 'SRR13663756_1' || true)" gz2="$(_compress_if_exists 'SRR13663756_2' || true)" gzs="$(_compress_if_exists 'SRR13663756' || true)" fasterq-dump --split-files "SRR13663757" gz1="$(_compress_if_exists 'SRR13663757_1' || true)" gz2="$(_compress_if_exists 'SRR13663757_2' || true)" gzs="$(_compress_if_exists 'SRR13663757' || true)" fasterq-dump --split-files "SRR13663758" gz1="$(_compress_if_exists 'SRR13663758_1' || true)" gz2="$(_compress_if_exists 'SRR13663758_2' || true)" gzs="$(_compress_if_exists 'SRR13663758' || true)" fasterq-dump --split-files "SRR13663759" gz1="$(_compress_if_exists 'SRR13663759_1' || true)" gz2="$(_compress_if_exists 'SRR13663759_2' || true)" gzs="$(_compress_if_exists 'SRR13663759' || true)" fasterq-dump --split-files "SRR13663760" gz1="$(_compress_if_exists 'SRR13663760_1' || true)" gz2="$(_compress_if_exists 'SRR13663760_2' || true)" gzs="$(_compress_if_exists 'SRR13663760' || true)" # Option B: Direct download (larger .sra files) curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663731/SRR13663731" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663732/SRR13663732" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663733/SRR13663733" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663734/SRR13663734" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663735/SRR13663735" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663736/SRR13663736" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663737/SRR13663737" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663738/SRR13663738" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663739/SRR13663739" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663740/SRR13663740" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663741/SRR13663741" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663742/SRR13663742" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663743/SRR13663743" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663744/SRR13663744" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663745/SRR13663745" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663746/SRR13663746" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663747/SRR13663747" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663748/SRR13663748" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663749/SRR13663749" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663750/SRR13663750" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663751/SRR13663751" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663752/SRR13663752" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663753/SRR13663753" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663754/SRR13663754" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663755/SRR13663755" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663756/SRR13663756" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663757/SRR13663757" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663758/SRR13663758" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663759/SRR13663759" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663760/SRR13663760" # --- Additional data files --- curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663746/SRR13663746" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663753/SRR13663753" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663754/SRR13663754" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663731/SRR13663731" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663738/SRR13663738" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663739/SRR13663739" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663755/SRR13663755" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663756/SRR13663756" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663757/SRR13663757" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663740/SRR13663740" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663741/SRR13663741" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663742/SRR13663742" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663758/SRR13663758" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663759/SRR13663759" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663760/SRR13663760" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663743/SRR13663743" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663744/SRR13663744" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663745/SRR13663745" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663747/SRR13663747" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663748/SRR13663748" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663749/SRR13663749" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663732/SRR13663732" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663733/SRR13663733" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663734/SRR13663734" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663750/SRR13663750" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663751/SRR13663751" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663752/SRR13663752" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663735/SRR13663735" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663736/SRR13663736" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13663737/SRR13663737" echo "Download complete. Files saved to $OUTDIR"