Download Geo Tar File Automatically From Linux/Unix

Question

[dfernan]

Hi,

I'd like to automatically download the tar files from the following links, does anyone knows how to do that?

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39977

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36375

Kind of like using wget...

Thanks!

[Ge]

check out the tool aspera. GEO supports it. http://www.ncbi.nlm.nih.gov/books/NBK47527/

The download speed will blow you away.

[Pappu]

You can also check out cURL: http://curl.haxx.se/

[quentin.delettre]

You can automate any task with CRON on unix plateforms.

Answer 1

[dfernan]

Never mind, just figured it out. I can go to the ftp site and do wget:

ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE39nnn/GSE39977/suppl/

wget 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE39nnn/GSE39977/suppl/GSE39977_RAW.tar'

Thanks!

[Sukhi Singh]

Check the parameter -b, love it, sends the download to background and generates log. Good for multiple downloads.

[dfernan]

Thanks for the suggestion!

[Shicheng Guo]

GEO should provide a automatical tools to download the data, such as fastq-dump

Answer 2

[Sean Davis]

Just a note that the GEOquery bioconductor package does this for a living, if you happen to be targeting R for further processing/analysis. See the help for getGEOSuppFiles() and getGEO().

Answer 3

[Bioinfotec]

wget -r -nH --cut-dirs=3 ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE39nnn/GSE39977/

The -r option in the wget command stands for "recursive," and tells wget to download files recursively from the specified FTP directory.

The --cut-dirs option tells wget to cut off the specified number of directories from the beginning of the directory hierarchy when saving the downloaded files. In the example command I provided, --cut-dirs=3 tells wget to remove the first three directories from the path of the downloaded files.