How to Install SPAdes in UBUNTU/LINUX

hello everyone and Welcome to our YouTube channel again uh today's video is about how you can install a genome assembler called that space this space is um very popular amongst the bionformatics and genomics community and you can uh use this to assemble your genome your transcriptome even it has option for the plasmids and metagenomic assembly as well uh so let let's look at uh how you can install the space on your B system uh so you can install Spades uh with two three different ways uh first is you can install using AP install command and to do that you just first always check the version available so with that you can do sorry apt cache policy and Spates and the available version is 3.13.1 uh but this is not the latest version so if you want to install this you can do that so do AP get and space so if you type this come on and press enter so it's going to install this version of space for you um I'm not going to do that that's why I commented the command um the other way is you can go to Google and download the latest binary files space genome assembler download and it will direct you to its GitHub page so you can go to the GitHub page and you can download the latest uh binary file so here I go to this one and I'm going to download this and I'm I'm going to download this file which is for the Linux I'm going to copy the link address and type this link and press enter and you can see I have downloaded this page for myself and I'm going to unzip it so if I go to space folder and pin so you can see we have all those uh executable files required to run the space and you can use these to to run the Spades uh for your samples uh so there is another way of uh installing Spades uh which is to build the source code uh so to do that um what you need to do is you need to go to the space GitHub page uh as we did before and then download this source code so you can which download whichever of these two you like so let's download this one and type w get and paste this link and it will download this uh file for you and so before uh we go to the download part what we need to do is we need to um install some prerequisite libraries for it I have all those libraries installed with me so I'm not going to um install those libraries but I have shared uh the details how you can install those prerequisite libraries uh in the description so so first you need to install those libraries and then you can uh build the source code of spad uh to build the source code first you need to unzip uh the file we just downloaded which was waran 3 something so it's going to take just couple of minutes to unip all those files and once these are unzipped then we're going to go towards the further step so now you can see that we have unzipped that folder now go to that folder uh so we need to go to this assembl folder and uh you can see that uh we got multiple files here um so what we need to do is we need to uh compile this file and to compile that uh you need to type Spates underscore compile Dosh and this will uh going to compile all the servers Cod or build that uh the code from the uh source code um but um this command will uh make all those executable files in a bin folder uh which will be in this page folder uh if you want to build your uh space uh in your user local bin folder what you or some any other folder what you can do is uh you can give them the path user local bin so if you type this uh or uh if you want to type any other uh po you want uh your space to be built in that folder uh you can type that part and when you press enter um it's going to uh build the source code for you I'm just typing this and I'm going to press enter it's going to take some time like 5 to 10 minutes or maybe 15 minutes and after that you will be able to uh install space in your obento system uh so as you can see the software has been installed um and you can simply check it uh by typing the ls uh and you can see there is um all these um files for uh space which you can use to run the space software uh thank you very much and please don't forget to subscribe our YouTube channel

Channel: 23rdPairLab

Views: 205

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Id: _WnUoRN67bU

Length: 6min 35sec (395 seconds)

Published: Wed Oct 04 2023