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When transferring files between your computer and a remote server, you always need to execute the command on your local computer. This is because your personal computer does not have an entry in the global hostname database (a.k.a. the , whereas the remote computer does. The global Domain Name Service, or DNS), whereas the remote computer does database maps full host names to their IP (Internet Protocol) address. Computers that can be accessed from anywhere on the Internet have their host names registered in DNS. |
wget (web get)
The wget <url> command lets you retrieve the contents of a valid Internet URL (e.g. http, https, ftp).
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- ln -s <path> says to create a symbolic link link (symlink) to the specified file (or directory) in the current directory
- always use the -s option to avoid creating a hard link, which behaves quite differently
- the default link name corresponds to the last name component in <path>
- you can name the link file differently by supplying an optional link_file_name.
- it is best to change into (cd) the directory where you want the link before executing ln -s
- a symbolic link can be deleted without affecting the linked-to file
- the -f (force) option says to overwrite any existing symbolic link with the same name
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- find returns a list of matching file paths on its standard output
- ln wants its files listed as arguments, not on standard input
- so the paths are piped to the standard input of xargs
- xargs takes the data on its standard input and calls the specified function (here ln -sf -t .) with that data as the function's argument list.
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The cutadapt usage says an input.fastq file is a required argument:
But again, reading a bit further we see:
This says that the input.fastq file can be provided in one of three compression formats. And the usage also suggests input can be specified in 2 ways:
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Where does cutadapt write its diagnostic output by default? How can that be changed?
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The cutadapt usage doesn't say anything directly about diagnostics:
But again, reading in the Output: options section:
Careful reading of this suggests that:
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