@Srikan wget parses the HTML to find the links that it contains and recursively downloads (a selection of) those links. – Gilles Oct 6 '16 at 21:05 If the files don't have any internal links, then does recursive download fail to get all the files. I guess most of you, developers, use any VCS, and I hope some of you use Git.Do you have any tip or trick how to get a download URL for a single file in a repository? I don't want the URL for displaying the raw file; in case of binaries it's for nothing. Feb 13, 2014 The powerful curl command line tool can be used to download files from just about any remote server. Longtime command line users know this can be useful for a wide variety of situations, but to keep things simple, many will find that downloading a file with curl. The curl project mostly provides source packages. Other packages are kindly provided by external persons and organizations. Source Archives. Curl 7.61.1, Released on the 5th of September 2018.Changelog for 7.61.1. Include images found in current page, when enabled, sends to the download manager also the images which are visible in the page, rather than the linked objects only, e.g. The thumbnail-sized images in a gallery plus the big images or movies they're linked with.
Question: Download All The Bacterial Genomes From Ncbi
10
7.2 years ago by
Dear all!
i want to download all the bacterial genomes from NCBI. when i check the number of available genomes at NCBI at this link http://www.ncbi.nlm.nih.gov/genome/browse/it shows the total number of bacterial genomes as 3791. but when i download them from ftp-site ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/ using this command
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/all.fna.tar.gz
it downloads only less than 2300 genomes. can anyone tell me why is that, and how can i download all of them?
ADD COMMENT • link • modified 2.1 years ago by Biostar ♦♦ 20 • written 7.2 years ago by rehma.ar • 230
4
A lot of genomes don't have any data. Look at the Chr column in the table, if there is no number then no sequence is available.
ADD REPLY • link modified 3.3 years ago • written 7.2 years ago by Asaf ♦ 7.1k
Terminal
Hey
I like using Terminal, it is usually much more efficient and a lot quicker then the normal methods you use on your Mac. This post is about one widely used tool on UNIX and Linux systems, wget. Wget is a small program that can download files and folders to your computer through Terminal. There is already program similar to wget on your Mac, it is called curl. Although they do the same task, I prefer wget. When I tried curl on my computer it threw up lots of errors and problems. This post will tell you how to install wget and some simple basic usage. It is simple to do and really doesn’t take that long. I can’t take full credit for this tip, I took some of the steps from asitis.
The first step is to download the source code. Head over to the offical site and download the code directly. Once as you have downloaded the package unzip it. There will be a lots of funky files and folders. Thankfully we don’t have to deal with any of them. Open up Terminal and navigate to the folder wget is extracted in. For example:
cd ~/desktop/temp/wget-1.9.1
We know need to configure the package for your computer and install it. This is done slightly differently to normal packages and folders you may experience. In Terminal again type the following:
./configure
This will configure the packages and files for your computer. Then type:
make
![Mac Mac](/uploads/1/2/6/4/126433865/415359489.png)
This will make the files into a single binary file for use on your computer. Finally type:
sudo make install
This will copy the binary file into the correct location on your computer. Since the folder wget will copy into is a protected system folder, you will have to use the sudo command and an administrator password.
You have successfully installed wget. For example you can use wget to download zip files using the following command in Terminal.
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Wget Linux Download File
wget http://www.file.com/location/file.zip
Wget is designed to download files and web pages in Terminal but it can do a whole lot more. For some reason the link to the man page does not seem to work. So you can visit this URL instead.
Download Wget For Mac
You can do hundreds of different things with wget. It really is quite powerful and very easy to use. I recommend reading the man page to find out how to use it. You probably wont use it every day, but for anyone who likes using Terminal, or wants to play around with some more Unix commands, wget is a very fun one to use. If I remember correctly there was an old joke where you type “wget *.*” to download the entire internet.
If you want to take your skills with Terminal a bit further I recommend you check out the Terminal Category on this site. If you fancy reading a book there is a couple on Amazon that I regularly see mentioned and recommend, O’reilly Unix Geeks and Unix Under the Hood both are designed for Mac OS X and take Terminal further.
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