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I am trying to download files from this website.
The URL is: http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE48191&format=file
When I use this command:
wget http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE48191&format=file
I get only index.html?acc=GSE48191 which is some kind of binary format.
How can I download the files from this HTTP site?
I think your ? gets interpreted by shell (Correction by vinc17: more likely, it's the & which gets interpreted).
Just try with simple quotes around your URL:
wget 'http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE48191&format=file'
Note that the file you are requesting is a .tar file but the above command will save it as index.html?acc=GSE48191&format=file. To have it correctly named, you can either rename it to .tar:
mv 'index.html?acc=GSE48191&format=file' GSE4819.tar
Or you can give the name as an option to wget:
wget -O GSE48191.tar 'http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE48191&format=file'
The above command will save the downloaded file as GSE48191.tar directly.
? as a wildcard since nothing matches. The main problem is &: this will run the part that precedes (thus with an incomplete URL) in the background. But the solution is the same: to quote the URL.
.tar file) that contains the .gz files. Once you have downloaded it, run tar xvf GSE4819.tar to expand the archive and access the files.
Another way that might possibly work is by using this command:
wget -O nameOfTar.tar "http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE48191&format=file"
The -O command will specify the name to download to.
Of course, your initial problem is because the "&" was being interpreted by the shell, surrounding the URL with double quotes fixes the issue.
-O option is used to specify the name of the file in which dowloaded data is saved. It has no incidence on downloaded data (maybe that's what you meant, but I found it unclear).
& is interpreted by shell, and download of .tar file will fail.
None of these answers worked for me.
However, you can find GSE* folders within the NCBI ftp page:
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48191/suppl/
You can then copy the link address from that file and just do a simple wget:
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48191/suppl/GSE48191_RAW.tar
wget -O "name-you-want-to-save-as.format" http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE48191&format=file
That should get you the file you want to download to the current directory you are in.
wget: missing URL is what wget replies to that, because you are missing the argument to -O. Also, I think this probably doesn't solve the OP's problem anyway.
&, this answer doesn't work unless you add "" or '' around the URL.
Jan 8, 2018 at 2:33
From $ curl -G http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE48191
<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
<html><head>
<title>301 Moved Permanently</title>
</head><body>
<h1>Moved Permanently</h1>
<p>The document has moved <a href="https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE48191">here</a>.</p>
</body></html>
So you need to do
wget https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE48191
Notice the "s" after http. I tried it myself and it worked just fine.
What would help better is giving the page you got the link from which is: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE48191
Now with that page the clickable link is: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48191/suppl/GSE48191_RAW.tar
So use wget with the link is:
wget https://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48191/suppl/GSE48191_RAW.tar
