#!/usr/bin/env bash # Bulk download script for GSE34993 # Generated from Yeo Lab Publications Database # Total files: 35 OUTDIR="GSE34993" mkdir -p "$OUTDIR" cd "$OUTDIR" # --- GEO supplementary files --- wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE34nnn/GSE34993/suppl/GSE34993_RAW.tar" -O "GSE34993_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 "${stem}.fq.gz" return 0 fi return 1 } # Option A: Download via SRA Toolkit (recommended) fasterq-dump --split-files "SRR398195" gz1="$(_compress_if_exists 'SRR398195_1' || true)" gz2="$(_compress_if_exists 'SRR398195_2' || true)" gzs="$(_compress_if_exists 'SRR398195' || true)" fasterq-dump --split-files "SRR398196" gz1="$(_compress_if_exists 'SRR398196_1' || true)" gz2="$(_compress_if_exists 'SRR398196_2' || true)" gzs="$(_compress_if_exists 'SRR398196' || true)" fasterq-dump --split-files "SRR398197" gz1="$(_compress_if_exists 'SRR398197_1' || true)" gz2="$(_compress_if_exists 'SRR398197_2' || true)" gzs="$(_compress_if_exists 'SRR398197' || true)" fasterq-dump --split-files "SRR398198" gz1="$(_compress_if_exists 'SRR398198_1' || true)" gz2="$(_compress_if_exists 'SRR398198_2' || true)" gzs="$(_compress_if_exists 'SRR398198' || true)" fasterq-dump --split-files "SRR398199" gz1="$(_compress_if_exists 'SRR398199_1' || true)" gz2="$(_compress_if_exists 'SRR398199_2' || true)" gzs="$(_compress_if_exists 'SRR398199' || true)" fasterq-dump --split-files "SRR398200" gz1="$(_compress_if_exists 'SRR398200_1' || true)" gz2="$(_compress_if_exists 'SRR398200_2' || true)" gzs="$(_compress_if_exists 'SRR398200' || true)" fasterq-dump --split-files "SRR398201" gz1="$(_compress_if_exists 'SRR398201_1' || true)" gz2="$(_compress_if_exists 'SRR398201_2' || true)" gzs="$(_compress_if_exists 'SRR398201' || true)" fasterq-dump --split-files "SRR398202" gz1="$(_compress_if_exists 'SRR398202_1' || true)" gz2="$(_compress_if_exists 'SRR398202_2' || true)" gzs="$(_compress_if_exists 'SRR398202' || true)" fasterq-dump --split-files "SRR398203" gz1="$(_compress_if_exists 'SRR398203_1' || true)" gz2="$(_compress_if_exists 'SRR398203_2' || true)" gzs="$(_compress_if_exists 'SRR398203' || true)" fasterq-dump --split-files "SRR398204" gz1="$(_compress_if_exists 'SRR398204_1' || true)" gz2="$(_compress_if_exists 'SRR398204_2' || true)" gzs="$(_compress_if_exists 'SRR398204' || true)" fasterq-dump --split-files "SRR398205" gz1="$(_compress_if_exists 'SRR398205_1' || true)" gz2="$(_compress_if_exists 'SRR398205_2' || true)" gzs="$(_compress_if_exists 'SRR398205' || true)" fasterq-dump --split-files "SRR398206" gz1="$(_compress_if_exists 'SRR398206_1' || true)" gz2="$(_compress_if_exists 'SRR398206_2' || true)" gzs="$(_compress_if_exists 'SRR398206' || true)" fasterq-dump --split-files "SRR398207" gz1="$(_compress_if_exists 'SRR398207_1' || true)" gz2="$(_compress_if_exists 'SRR398207_2' || true)" gzs="$(_compress_if_exists 'SRR398207' || true)" fasterq-dump --split-files "SRR398208" gz1="$(_compress_if_exists 'SRR398208_1' || true)" gz2="$(_compress_if_exists 'SRR398208_2' || true)" gzs="$(_compress_if_exists 'SRR398208' || true)" fasterq-dump --split-files "SRR398209" gz1="$(_compress_if_exists 'SRR398209_1' || true)" gz2="$(_compress_if_exists 'SRR398209_2' || true)" gzs="$(_compress_if_exists 'SRR398209' || true)" # Option B: Direct download (larger .sra files) curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/398/SRR398195/SRR398195.2" curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/398/SRR398196/SRR398196.2" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398197/SRR398197" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398198/SRR398198" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398199/SRR398199" curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/398/SRR398200/SRR398200.2" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398201/SRR398201" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398202/SRR398202" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398203/SRR398203" curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/398/SRR398204/SRR398204.2" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398205/SRR398205" curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/398/SRR398206/SRR398206.2" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398207/SRR398207" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398208/SRR398208" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398209/SRR398209" # --- Additional data files --- curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/398/SRR398195/SRR398195.2" curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/398/SRR398196/SRR398196.2" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398197/SRR398197" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398198/SRR398198" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398199/SRR398199" curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/398/SRR398200/SRR398200.2" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398201/SRR398201" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398202/SRR398202" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398203/SRR398203" curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/398/SRR398204/SRR398204.2" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398205/SRR398205" curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/398/SRR398206/SRR398206.2" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398207/SRR398207" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398208/SRR398208" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398209/SRR398209" curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/398/SRR398196/SRR398196.2" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398201/SRR398201" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398202/SRR398202" curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR398203/SRR398203" echo "Download complete. Files saved to $OUTDIR"