{"id":412,"date":"2015-11-30T00:50:46","date_gmt":"2015-11-30T00:50:46","guid":{"rendered":"http:\/\/www.abyteofcommonsense.com\/?p=412"},"modified":"2015-11-30T00:50:46","modified_gmt":"2015-11-30T00:50:46","slug":"using-the-mac-osx-command-line","status":"publish","type":"post","link":"http:\/\/www.abyteofcommonsense.com\/?p=412","title":{"rendered":"Using the mac OSX command line"},"content":{"rendered":"

The most sensible way to set up your working environment in the Mac command line when you want to do the same thing in multiple folders is to make sure you have labelled everything in the same way.\u00a0A handy hint here is that if you have terminal open, and you want to simply open more tabs that are in the same space you can use:<\/p>\n

Shell > New Tab > New Tab with Settings – Basic<\/strong><\/p><\/blockquote>\n

Now, if you’re going to use it to create multiple tabs, it’s important to be patient between opening tabs. Otherwise you’ll find that it hasn’t ‘logged on’ correctly into the target folder you want, and you’ll find yourself with a bunch of tabs into the home directory.<\/p>\n

Let’s say you want to run a bunch of blast searches, but first you need to do some basic formatting of your data, and move it around in the folders you have created. Using the commands from my post about blast<\/a>, you can use the symbol<\/p>\n

&&<\/strong><\/p><\/blockquote>\n

between each command. This is a conditional addition – so if one line fails, it’s ok. The process will stop, saving you precious processing time if you are editing more than one folder at a time (and you’ve left it for the weekend). If for some reason, you don’t care whether it finished correctly or not, you can use the symbol<\/p>\n

;<\/strong><\/p><\/blockquote>\n

In almost all cases, you are going to want to use &&. If you have any doubts about things running, you can<\/p>\n

sudo<\/strong><\/p><\/blockquote>\n

commands. This requires you to put in your administrator password into terminal (the same one that you use to log into your machine). This word\u00a0makes your computer pretty much ignore any blocks there might be on your data being saved in any location. Only use it if you know you aren’t going to be doing anything super system altering! Otherwise you might come back, and have nothing left… Another note is that terminal will remember sudo being used for a time, so you can use it more than once in your list of commands.<\/p>\n","protected":false},"excerpt":{"rendered":"

The most sensible way to set up your working environment in the Mac command line when you want to do the same thing in multiple…<\/p>\n

Continue readingUsing the mac OSX command line<\/span><\/a><\/div>\n","protected":false},"author":2,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"spay_email":"","jetpack_publicize_message":"","jetpack_is_tweetstorm":false},"categories":[69],"tags":[70,72],"jetpack_featured_media_url":"","jetpack_publicize_connections":[],"jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/p6nzXS-6E","jetpack-related-posts":[{"id":410,"url":"http:\/\/www.abyteofcommonsense.com\/?p=410","url_meta":{"origin":412,"position":0},"title":"Creating a custom local Blast database from .fasta","date":"November 23, 2015","format":false,"excerpt":"All these commands are pretty simple to use, but I couldn't find really straight forward answers for why the hell I was getting errors, so here is my quick guide. I hope you find it useful. When you are creating a custom NCBI blast database to use, there's a couple\u2026","rel":"","context":"In "Bioinformatics"","img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":400,"url":"http:\/\/www.abyteofcommonsense.com\/?p=400","url_meta":{"origin":412,"position":1},"title":"Local NCBI BLAST problems? Some solutions for the unexperienced bioinformatician","date":"November 16, 2015","format":false,"excerpt":"Is local blast driving you nuts? Blast is a super powerful tool if you download it onto your own computer because you can blast more than one sequence at once, and not have to worry about the server dying on you. Having set it up both with the experience of\u2026","rel":"","context":"In "Bioinformatics"","img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":403,"url":"http:\/\/www.abyteofcommonsense.com\/?p=403","url_meta":{"origin":412,"position":2},"title":"How to deal with Blast output and Fasta to get what you need for MEGAN (using Qiime)","date":"November 18, 2015","format":false,"excerpt":"So... You have some sequence data from Illumina sequencing.\u00a0These are the two sets of files I have, one is forward reads, and the other is reverse. PP2_S1_L001_R2_001.fastq.gz PP2_S1_L001_R1_001.fastq.gz ... it's in fastaq.gz format. You want to upzip it, simple right? You want to use this command: gunzip --keep PP2_S1_L001_R2_001.fastq.gz But\u2026","rel":"","context":"In "Bioinformatics"","img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":465,"url":"http:\/\/www.abyteofcommonsense.com\/?p=465","url_meta":{"origin":412,"position":3},"title":"Blast(ed) MEGAN Round 2 - or what to do when you're running yet another blast","date":"April 5, 2016","format":false,"excerpt":"So MEGAN can be a bit annoying at times. As can Blast outputs required by MEGAN. Because I'm particularly interested in the alignments produced, and want to create a consensus sequence for designing primers, I need to run blast again from what I did the other day. This time, I've\u2026","rel":"","context":"In "Bioinformatics"","img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":837,"url":"http:\/\/www.abyteofcommonsense.com\/?p=837","url_meta":{"origin":412,"position":4},"title":"7 Ways to Make Money Online","date":"November 28, 2018","format":false,"excerpt":"We'd all like to receive free things, right? Well here I've listed 3 ways you can sign up to be on Product Testing lists, and 4 surveys. All of these are available to Australians, although The Black Box is limited to only three states. Product Testing Woolworths Bunch - You'll\u2026","rel":"","context":"In "Finance"","img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":127,"url":"http:\/\/www.abyteofcommonsense.com\/?p=127","url_meta":{"origin":412,"position":5},"title":"10 hints on how to succeed on Tinder","date":"March 27, 2014","format":false,"excerpt":"So I've been using Tinder for a couple of weeks now. So far, I have been through hundreds of girls and a handful of men (huh? I was confused too). Read on for my guide to Tinder. 1. Don't be disheartened if you don't get replies right away (or at\u2026","rel":"","context":"In "Dating"","img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]}],"_links":{"self":[{"href":"http:\/\/www.abyteofcommonsense.com\/index.php?rest_route=\/wp\/v2\/posts\/412"}],"collection":[{"href":"http:\/\/www.abyteofcommonsense.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.abyteofcommonsense.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.abyteofcommonsense.com\/index.php?rest_route=\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"http:\/\/www.abyteofcommonsense.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=412"}],"version-history":[{"count":1,"href":"http:\/\/www.abyteofcommonsense.com\/index.php?rest_route=\/wp\/v2\/posts\/412\/revisions"}],"predecessor-version":[{"id":413,"href":"http:\/\/www.abyteofcommonsense.com\/index.php?rest_route=\/wp\/v2\/posts\/412\/revisions\/413"}],"wp:attachment":[{"href":"http:\/\/www.abyteofcommonsense.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=412"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.abyteofcommonsense.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=412"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.abyteofcommonsense.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=412"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}