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How to Install EDirect on Mac, Unix, or Linux

This turial shows you to NCBI's Entrez Direct, , programs a Mac The procedure is the same for Unix and machines


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You will install, and run the edirect programs, from the Terminal app In most cases, your default directory will be /Users/username, and that's as good a place as any to install EDirect All I need now is the bit of text containing the installation commands That text is in the EDirect documentation in our online Books database; just search in your browser for ncbi edirect and you will get to this chapter https://www

ncbinlmnihgov/books/NBK179288/ This is a big and immensely helpful document that allows you to take full advantage of EDirect's capabilities For now I'll just scroll down to the Installation section and copy this text

Back to my terminal window, I'll paste that in, hit Enter, and away it goes You should quickly get to this setupsh shell script Hit Enter again to run that script, and it will stop on this message about Trying to establish local installations of any missing Perl modules It may sit there for a minute or so, then will declare that Entrez Direct has been successfully downloaded and installed

You are also prompted to set a PATH variable so that you can run the edirect programs from any directory I recommend running the echo command as presented, which is as easy as copying that line beginning with echo, pasting it in at the prompt and hitting Enter Okay, that's done, and I now have a new directory called edirect, and I'll very quickly show you what's in that directory Here you have the EDirect programs, such as efetch, esearch, xtract, etc Now let's check to see if the EDirect programs are working

One way to do that is to type a program name and ask for the version number I'll do that by typing, esearch dash version, and we see not only that I've got version 980, but this also means that the EDirect programs are properly installed You likely have a newer version because EDirect is updated fairly often — check the end of the EDirect documentation to see how to get on an email list that will notify you of updates Another useful command is the program name a space and dash help

I'll type efetch dash help the pipe symbol, |, then the program more, just so the documentation doesn't scroll all the way to the bottom This is a quick way to see command line options without having to go to the documentation on the web Hitting the space bar moves you through the text Okay, all seems well, but what the heck, let's run a real efetch command to show you how easy it is to use This command retreives a protein record in FASTA format and sends that to a file called np

faa, or whatever name you give it All I need is the accession number from the NCBI Protein database I'll use NP_000302 dot 1 efetch -db protein -id np_0003021 -format fasta > npfaa So I've run that, and I'll use the cat command to view that FASTA file

And there it is That's it You're now ready to run EDirect on your Mac In the YouTube Description of this video you will find some useful links, and if you have any questions, please write to, [email protected]


Source: Youtube

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