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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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@@ -35,7 +35,7 @@ gzip is a utility for compressing and decompressing individual files. To compres
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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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@@ -51,9 +51,9 @@ To create a gzipped disk file tar archive, use
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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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@@ -65,7 +65,7 @@ To unpack files from a 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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@@ -79,13 +79,13 @@ Some commands give you an output to your screen, but you would have preferred it
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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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@@ -114,8 +114,8 @@ Remember the command `grep`? We can pipe other commands to it, to refine searche
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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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