#!/usr/bin/env bash # Bulk download script for GSE290765 # Generated from Yeo Lab Knowledgebase # Total files: 24 OUTDIR=GSE290765 mkdir -p "$OUTDIR" cd "$OUTDIR" # --- 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 "${stem}.fq.gz" return 0 fi return 1 } # Option A: Download via SRA Toolkit (recommended) fasterq-dump --split-files SRR32524333 gz1="$(_compress_if_exists SRR32524333_1 || true)" gz2="$(_compress_if_exists SRR32524333_2 || true)" gzs="$(_compress_if_exists SRR32524333 || true)" fasterq-dump --split-files SRR32524334 gz1="$(_compress_if_exists SRR32524334_1 || true)" gz2="$(_compress_if_exists SRR32524334_2 || true)" gzs="$(_compress_if_exists SRR32524334 || true)" fasterq-dump --split-files SRR32524335 gz1="$(_compress_if_exists SRR32524335_1 || true)" gz2="$(_compress_if_exists SRR32524335_2 || true)" gzs="$(_compress_if_exists SRR32524335 || true)" fasterq-dump --split-files SRR32524336 gz1="$(_compress_if_exists SRR32524336_1 || true)" gz2="$(_compress_if_exists SRR32524336_2 || true)" gzs="$(_compress_if_exists SRR32524336 || true)" fasterq-dump --split-files SRR32524337 gz1="$(_compress_if_exists SRR32524337_1 || true)" gz2="$(_compress_if_exists SRR32524337_2 || true)" gzs="$(_compress_if_exists SRR32524337 || true)" fasterq-dump --split-files SRR32524338 gz1="$(_compress_if_exists SRR32524338_1 || true)" gz2="$(_compress_if_exists SRR32524338_2 || true)" gzs="$(_compress_if_exists SRR32524338 || true)" fasterq-dump --split-files SRR32524339 gz1="$(_compress_if_exists SRR32524339_1 || true)" gz2="$(_compress_if_exists SRR32524339_2 || true)" gzs="$(_compress_if_exists SRR32524339 || true)" fasterq-dump --split-files SRR32524340 gz1="$(_compress_if_exists SRR32524340_1 || true)" gz2="$(_compress_if_exists SRR32524340_2 || true)" gzs="$(_compress_if_exists SRR32524340 || true)" fasterq-dump --split-files SRR32524341 gz1="$(_compress_if_exists SRR32524341_1 || true)" gz2="$(_compress_if_exists SRR32524341_2 || true)" gzs="$(_compress_if_exists SRR32524341 || true)" fasterq-dump --split-files SRR32524342 gz1="$(_compress_if_exists SRR32524342_1 || true)" gz2="$(_compress_if_exists SRR32524342_2 || true)" gzs="$(_compress_if_exists SRR32524342 || true)" fasterq-dump --split-files SRR32524343 gz1="$(_compress_if_exists SRR32524343_1 || true)" gz2="$(_compress_if_exists SRR32524343_2 || true)" gzs="$(_compress_if_exists SRR32524343 || true)" fasterq-dump --split-files SRR32524344 gz1="$(_compress_if_exists SRR32524344_1 || true)" gz2="$(_compress_if_exists SRR32524344_2 || true)" gzs="$(_compress_if_exists SRR32524344 || true)" # Option B: Direct download (larger .sra files) curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32524/SRR32524333/SRR32524333.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32524/SRR32524334/SRR32524334.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32524/SRR32524335/SRR32524335.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32524/SRR32524336/SRR32524336.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32524/SRR32524337/SRR32524337.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32524/SRR32524338/SRR32524338.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32524/SRR32524339/SRR32524339.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32524/SRR32524340/SRR32524340.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32524/SRR32524341/SRR32524341.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32524/SRR32524342/SRR32524342.lite.1 curl -L -O -C - https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR32524343/SRR32524343 curl -L -O -C - https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR32524344/SRR32524344 # --- Additional data files --- curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32524/SRR32524333/SRR32524333.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32524/SRR32524334/SRR32524334.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32524/SRR32524335/SRR32524335.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32524/SRR32524336/SRR32524336.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32524/SRR32524337/SRR32524337.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32524/SRR32524338/SRR32524338.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32524/SRR32524339/SRR32524339.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32524/SRR32524340/SRR32524340.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32524/SRR32524341/SRR32524341.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32524/SRR32524342/SRR32524342.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32524/SRR32524343/SRR32524343.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32524/SRR32524344/SRR32524344.lite.1 echo "Download complete. Files saved to $OUTDIR"