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Jonas Ohlsson
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fix typos.
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unix/fully_walking.md

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# Introduction to Unix (continued)
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In this part of the Unix tutorial, you will learn to download files, compress and decompress them, and combining commands
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In this part of the Unix tutorial, you will learn to download files, compress and decompress them, and combine commands.
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## Download files
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`wget` can be used to download files from internet and store them. The following downloads and stores a file called to the current directory.
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`wget` can be used to download files from the internet and store them.
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`wget https://raw.githubusercontent.com/HadrienG/tutorials/master/LICENSE`
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will download the file that is located at the above URL on the internet, and put it **in the current directory**. This is the license under which this course is released. Open in and read it if you like!
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will download the file that is located at the above URL on the internet, and put it **in the current directory**. This is the license under which this course is released. Open it and read it if you like!
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The `-O` option can be used to change the output file name.
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`gzip filename`
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The filename will be deleted and replaced by a compressed file called filename.gz To reverse the compression process, use:
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The filename will be deleted and replaced by a compressed file called filename.gz. To reverse the compression process, use:
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`gzip -d filename.gz`
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`tar -czvf archivename filenames`
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where archivename will usually have a .tar .gz extension
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where archivename will usually have a .tar.gz extension
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The c option means create, the v option means verbose (output filenames as they are archived), and option f means file.
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The c option means create, the v option means verbose (output filenames as they are archived), option f means file, and z means that the tar archive should be gzip compressed.
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To list the contents of a gzipped tar archive, use
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Try to archive the folder `Module_Unix` from the previous exercise!
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You will notice a file called tutorials.tar.bz2 in your home directory. This is also a compressed archive, but compressed in the bzip format. Read the tar manual and find a way to decompress it
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You will notice a file called tutorials.tar.bz2 in your home directory. This is also a compressed archive, but compressed in the bzip format. Read the tar manual and find a way to decompress it.
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Hint: you can read the manual for any command using `man`
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The output from a command normally intended for standard output (that is, your screen) can be easily diverted to a file instead. This capability is known as output redirection:
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If the notation `> file` is appended to any command that normally writes its output to standard output, the output of that command will be written to file instead of your terminal
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If the notation `> file` is appended to any command that normally writes its output to standard output, the output of that command will be written to file instead of your terminal.
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I.e, the following who command:
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`who > users.txt`
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No output appears at the terminal. This is because the output has been redirected into the specified file.
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No output appears at the terminal. This is because the output has been redirected into the specified file.
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`less users.txt`
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`ls -l ngs_course_data | grep "Jan"`
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will only give you the files and directories created in January
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will only give you the files and directories created in January.
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Tip: There are various options you can use with the grep command, look at the manual!
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Pipes are extremely useful to connect various bioinformatics softwares together. We'll use them extensively later.
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Pipes are extremely useful to connect various bioinformatics software together. We'll use them extensively later.

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