#!/usr/bin/env bash # Bulk download script for GSE145805 # Generated from Yeo Lab Knowledgebase # Total files: 49 OUTDIR=GSE145805 mkdir -p "$OUTDIR" cd "$OUTDIR" # --- GEO supplementary files --- wget -nc ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE145nnn/GSE145805/suppl/GSE145805_RAW.tar -O GSE145805_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 "${stem}.fq.gz" return 0 fi return 1 } # Option A: Download via SRA Toolkit (recommended) fasterq-dump --split-files SRR11164860 gz1="$(_compress_if_exists SRR11164860_1 || true)" gz2="$(_compress_if_exists SRR11164860_2 || true)" gzs="$(_compress_if_exists SRR11164860 || true)" fasterq-dump --split-files SRR11164861 gz1="$(_compress_if_exists SRR11164861_1 || true)" gz2="$(_compress_if_exists SRR11164861_2 || true)" gzs="$(_compress_if_exists SRR11164861 || true)" fasterq-dump --split-files SRR11164862 gz1="$(_compress_if_exists SRR11164862_1 || true)" gz2="$(_compress_if_exists SRR11164862_2 || true)" gzs="$(_compress_if_exists SRR11164862 || true)" fasterq-dump --split-files SRR11164863 gz1="$(_compress_if_exists SRR11164863_1 || true)" gz2="$(_compress_if_exists SRR11164863_2 || true)" gzs="$(_compress_if_exists SRR11164863 || true)" fasterq-dump --split-files SRR11164864 gz1="$(_compress_if_exists SRR11164864_1 || true)" gz2="$(_compress_if_exists SRR11164864_2 || true)" gzs="$(_compress_if_exists SRR11164864 || true)" fasterq-dump --split-files SRR11164865 gz1="$(_compress_if_exists SRR11164865_1 || true)" gz2="$(_compress_if_exists SRR11164865_2 || true)" gzs="$(_compress_if_exists SRR11164865 || true)" fasterq-dump --split-files SRR11164866 gz1="$(_compress_if_exists SRR11164866_1 || true)" gz2="$(_compress_if_exists SRR11164866_2 || true)" gzs="$(_compress_if_exists SRR11164866 || true)" fasterq-dump --split-files SRR11164867 gz1="$(_compress_if_exists SRR11164867_1 || true)" gz2="$(_compress_if_exists SRR11164867_2 || true)" gzs="$(_compress_if_exists SRR11164867 || true)" fasterq-dump --split-files SRR11164868 gz1="$(_compress_if_exists SRR11164868_1 || true)" gz2="$(_compress_if_exists SRR11164868_2 || true)" gzs="$(_compress_if_exists SRR11164868 || true)" fasterq-dump --split-files SRR11164869 gz1="$(_compress_if_exists SRR11164869_1 || true)" gz2="$(_compress_if_exists SRR11164869_2 || true)" gzs="$(_compress_if_exists SRR11164869 || true)" fasterq-dump --split-files SRR11164870 gz1="$(_compress_if_exists SRR11164870_1 || true)" gz2="$(_compress_if_exists SRR11164870_2 || true)" gzs="$(_compress_if_exists SRR11164870 || true)" fasterq-dump --split-files SRR11164871 gz1="$(_compress_if_exists SRR11164871_1 || true)" gz2="$(_compress_if_exists SRR11164871_2 || true)" gzs="$(_compress_if_exists SRR11164871 || true)" fasterq-dump --split-files SRR11164872 gz1="$(_compress_if_exists SRR11164872_1 || true)" gz2="$(_compress_if_exists SRR11164872_2 || true)" gzs="$(_compress_if_exists SRR11164872 || true)" fasterq-dump --split-files SRR11164873 gz1="$(_compress_if_exists SRR11164873_1 || true)" gz2="$(_compress_if_exists SRR11164873_2 || true)" gzs="$(_compress_if_exists SRR11164873 || true)" fasterq-dump --split-files SRR11164874 gz1="$(_compress_if_exists SRR11164874_1 || true)" gz2="$(_compress_if_exists SRR11164874_2 || true)" gzs="$(_compress_if_exists SRR11164874 || true)" fasterq-dump --split-files SRR11164875 gz1="$(_compress_if_exists SRR11164875_1 || true)" gz2="$(_compress_if_exists SRR11164875_2 || true)" gzs="$(_compress_if_exists SRR11164875 || true)" fasterq-dump --split-files SRR11164876 gz1="$(_compress_if_exists SRR11164876_1 || true)" gz2="$(_compress_if_exists SRR11164876_2 || true)" gzs="$(_compress_if_exists SRR11164876 || true)" fasterq-dump --split-files SRR11164877 gz1="$(_compress_if_exists SRR11164877_1 || true)" gz2="$(_compress_if_exists SRR11164877_2 || true)" gzs="$(_compress_if_exists SRR11164877 || true)" fasterq-dump --split-files SRR11164878 gz1="$(_compress_if_exists SRR11164878_1 || true)" gz2="$(_compress_if_exists SRR11164878_2 || true)" gzs="$(_compress_if_exists SRR11164878 || true)" fasterq-dump --split-files SRR11164879 gz1="$(_compress_if_exists SRR11164879_1 || true)" gz2="$(_compress_if_exists SRR11164879_2 || true)" gzs="$(_compress_if_exists SRR11164879 || true)" fasterq-dump --split-files SRR11164880 gz1="$(_compress_if_exists SRR11164880_1 || true)" gz2="$(_compress_if_exists SRR11164880_2 || true)" gzs="$(_compress_if_exists SRR11164880 || true)" fasterq-dump --split-files SRR11164881 gz1="$(_compress_if_exists SRR11164881_1 || true)" gz2="$(_compress_if_exists SRR11164881_2 || true)" gzs="$(_compress_if_exists SRR11164881 || true)" fasterq-dump --split-files SRR11164882 gz1="$(_compress_if_exists SRR11164882_1 || true)" gz2="$(_compress_if_exists SRR11164882_2 || true)" gzs="$(_compress_if_exists SRR11164882 || true)" fasterq-dump --split-files SRR11164883 gz1="$(_compress_if_exists SRR11164883_1 || true)" gz2="$(_compress_if_exists SRR11164883_2 || true)" gzs="$(_compress_if_exists SRR11164883 || true)" # Option B: Direct download (larger .sra files) curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164860/SRR11164860.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164861/SRR11164861.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164862/SRR11164862.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164863/SRR11164863.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164864/SRR11164864.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1211/SRR011/164/SRR11164865/SRR11164865.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164866/SRR11164866.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164867/SRR11164867.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos9/sra-pub-zq-922/SRR011/11164/SRR11164868/SRR11164868.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos9/sra-pub-zq-922/SRR011/11164/SRR11164869/SRR11164869.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164870/SRR11164870.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164871/SRR11164871.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164872/SRR11164872.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164873/SRR11164873.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos9/sra-pub-zq-922/SRR011/11164/SRR11164874/SRR11164874.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164875/SRR11164875.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164876/SRR11164876.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1211/SRR011/164/SRR11164877/SRR11164877.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164878/SRR11164878.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos9/sra-pub-zq-922/SRR011/11164/SRR11164879/SRR11164879.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164880/SRR11164880.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164881/SRR11164881.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164882/SRR11164882.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164883/SRR11164883.lite.1 # --- Additional data files --- curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164860/SRR11164860.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164861/SRR11164861.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164862/SRR11164862.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164863/SRR11164863.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164864/SRR11164864.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1211/SRR011/164/SRR11164865/SRR11164865.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164866/SRR11164866.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164867/SRR11164867.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos9/sra-pub-zq-922/SRR011/11164/SRR11164868/SRR11164868.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos9/sra-pub-zq-922/SRR011/11164/SRR11164869/SRR11164869.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164870/SRR11164870.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164871/SRR11164871.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164872/SRR11164872.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164873/SRR11164873.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos9/sra-pub-zq-922/SRR011/11164/SRR11164874/SRR11164874.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164875/SRR11164875.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164876/SRR11164876.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1211/SRR011/164/SRR11164877/SRR11164877.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164878/SRR11164878.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos9/sra-pub-zq-922/SRR011/11164/SRR11164879/SRR11164879.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164880/SRR11164880.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164881/SRR11164881.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164882/SRR11164882.lite.1 curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos12/sra-pub-zq-1216/SRR011/11164/SRR11164883/SRR11164883.lite.1 echo "Download complete. Files saved to $OUTDIR"