#!/usr/bin/env bash # Bulk download script for GSE254209 # Generated from Yeo Lab Knowledgebase # Total files: 25 OUTDIR=GSE254209 mkdir -p "$OUTDIR" cd "$OUTDIR" # --- GEO supplementary files --- wget -nc ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE254nnn/GSE254209/suppl/GSE254209_RAW.tar -O GSE254209_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 "${stem}.fq.gz" return 0 fi return 1 } # Option A: Download via SRA Toolkit (recommended) fasterq-dump --split-files SRR27726257 gz1="$(_compress_if_exists SRR27726257_1 || true)" gz2="$(_compress_if_exists SRR27726257_2 || true)" gzs="$(_compress_if_exists SRR27726257 || true)" fasterq-dump --split-files SRR27726258 gz1="$(_compress_if_exists SRR27726258_1 || true)" gz2="$(_compress_if_exists SRR27726258_2 || true)" gzs="$(_compress_if_exists SRR27726258 || true)" fasterq-dump --split-files SRR27726259 gz1="$(_compress_if_exists SRR27726259_1 || true)" gz2="$(_compress_if_exists SRR27726259_2 || true)" gzs="$(_compress_if_exists SRR27726259 || true)" fasterq-dump --split-files SRR27726260 gz1="$(_compress_if_exists SRR27726260_1 || true)" gz2="$(_compress_if_exists SRR27726260_2 || true)" gzs="$(_compress_if_exists SRR27726260 || true)" fasterq-dump --split-files SRR27726261 gz1="$(_compress_if_exists SRR27726261_1 || true)" gz2="$(_compress_if_exists SRR27726261_2 || true)" gzs="$(_compress_if_exists SRR27726261 || true)" fasterq-dump --split-files SRR27726262 gz1="$(_compress_if_exists SRR27726262_1 || true)" gz2="$(_compress_if_exists SRR27726262_2 || true)" gzs="$(_compress_if_exists SRR27726262 || true)" fasterq-dump --split-files SRR27726263 gz1="$(_compress_if_exists SRR27726263_1 || true)" gz2="$(_compress_if_exists SRR27726263_2 || true)" gzs="$(_compress_if_exists SRR27726263 || true)" fasterq-dump --split-files SRR27726264 gz1="$(_compress_if_exists SRR27726264_1 || true)" gz2="$(_compress_if_exists SRR27726264_2 || true)" gzs="$(_compress_if_exists SRR27726264 || true)" fasterq-dump --split-files SRR27726265 gz1="$(_compress_if_exists SRR27726265_1 || true)" gz2="$(_compress_if_exists SRR27726265_2 || true)" gzs="$(_compress_if_exists SRR27726265 || true)" fasterq-dump --split-files SRR27726266 gz1="$(_compress_if_exists SRR27726266_1 || true)" gz2="$(_compress_if_exists SRR27726266_2 || true)" gzs="$(_compress_if_exists SRR27726266 || true)" fasterq-dump --split-files SRR27726267 gz1="$(_compress_if_exists SRR27726267_1 || true)" gz2="$(_compress_if_exists SRR27726267_2 || true)" gzs="$(_compress_if_exists SRR27726267 || true)" fasterq-dump --split-files SRR27726268 gz1="$(_compress_if_exists SRR27726268_1 || true)" gz2="$(_compress_if_exists SRR27726268_2 || true)" gzs="$(_compress_if_exists SRR27726268 || true)" # Option B: Direct download (larger .sra files) curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726257/SRR27726257.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726258/SRR27726258.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726259/SRR27726259.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726260/SRR27726260.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726261/SRR27726261.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726262/SRR27726262.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726263/SRR27726263.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726264/SRR27726264.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726265/SRR27726265.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726266/SRR27726266.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726267/SRR27726267.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726268/SRR27726268.lite.1 # --- Additional data files --- curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726257/SRR27726257.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726258/SRR27726258.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726259/SRR27726259.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726260/SRR27726260.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726261/SRR27726261.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726262/SRR27726262.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726263/SRR27726263.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726264/SRR27726264.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726265/SRR27726265.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726266/SRR27726266.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726267/SRR27726267.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726268/SRR27726268.lite.1 echo "Download complete. Files saved to $OUTDIR"